باستانیان

از ویکی‌پدیا، دانشنامهٔ آزاد
پرش به: ناوبری، جستجو
فارسی English
باستانیان
محدوده زمانی: دیرینه‌آرکئن[۱] - امروز
هالوباکتری (شورباکتری). هر یاختهٔ آن در حدود ۵ میکرون درازا دارد.
طبقه‌بندی علمی
دامنه: نودیوارکان[۲]
فرمانرو: باستانیان
ووس، کاندلِر و ویلیس، ۱۹۹۰
شاخه‌ها

دماباستانیان
پَهن‌باستانیان
جوان‌باستانیان
کوتوله‌باستانیان

باستانیان یا آرکیا (Archaea) ( که به پارسی؛ باکتریهای باستانی هم ترجمه شده‌اند) گروهی از موجودات ریز تک‌یاخته‌ای هستند.

به هر یک از اعضاء گروه باستانیان یک باستانه (archaeon) گفته می‌شود.

باستانیان نیز همانند باکتری‌ها بدون هستک (پروکاریوت) هستند و در درون یاخته‌های خود هسته سلولی یا اندامک دیگری ندارند. در گذشته، این گروه به عنوان یک گروه غیرعادی از باکتری‌ها قلمداد می‌شد و از آن‌ها به عنوان آرکی‌باکتری‌ها (باستان‌باکتری‌ها) یاد می‌شد ولی از آن‌جا که تاریخ تکامل باستانیان و زیست‌شیمی آن‌ها بسیار متفاوت از دیگر اشکال زیستی است امروزه در سامانه سه‌فرمانرویی از آن‌ها به عنوان یک فرمانرو جدا یاد می‌شود.

در این سامانه که توسط کارل ووس[۳] ترتیب داده شده، سه گروه اصلی دودمان تکاملی عبارتند از باستانیان، هوهَسته‌ها (یوکاریوت‌ها) و باکتری‌ها. باستانیان خود به چهار شاخه بخش می‌شوند به نام‌های: دماباستانیان (Crenarchaeota)، پَهن‌باستانیان (Euryarchaeota)، جوان‌باستانیان (Korarchaeota) و کوتوله‌باستانیان (Nanoarchaeota). از این شاخه‌ها در مورد دو شاخهٔ اولی پژوهش‌های بسیار زیادی انجام شده‌است.

گونه‌هایی از باستانیان در اعماق اقیانوس‌ها و مغاکهای ظلمانی کشف شده‌اند و می‌توانند در جایی که حتی ذره‌ای از نور خورشید به آن نفوذ نمی‌کند، زنده بمانند. پژوهشگران احتمال می‌دهند که شاید علت دوام آن‌ها در چنین مکان‌هایی روش‌های ویژهٔ مصرف نفت برای ادامه زندگی باشد.[۴] آرکی باکتری‌ها معمولاً در شرایط سختی مانند دمای بالا، یا غلظت زیاد نمک زندگی می‌کنند. این شاخه کمتر از ۱۰۰ گونه را تشکیل می‌دهد؛ شامل باکتری‌های هوازی و غیر هوازی اند که با محیط‌های افراطی سازگار شده اند؛ پروکاریوت اند؛ از نظر ساختار دیواره و غشای سلول با سلول‌های یوکاریوت متفاوتند.

ژنتیک[ویرایش]

آرکی آها معمولاً دارای یک کروموزوم حلقوی هستند که اندازه آن میتواند به بزرگی ۵۱.۵۷.۴۹۲ جفت باز در Methanosarcina acetivorans باشد که بزرگترین ژنوم شناخته شده آرکی آها میباشد و يك دهم اين اندازه، به كوچكي ۴۹۰.۸۸۵ جفت باز در Nanoarchaeum equitans، کوچکترین ژنوم آرکی آی شناخته شده است که تخمین زده شده که شامل فقط ۵۳۷ ژن کد کننده پروتئین است. قطعات کوچک مستقل DNA به نام پلاسمید هم در آرکی آ یافت میشوند. پلاسمیدها میتوانند در فرایندی که شبیه کانژوگاسیون باکتری ها است با تماس فیزیکی بین سلول ها انتقال یابند.

نقش متانوژن‌ها[ویرایش]

متانوژن‌ها آرکه‌هایی هستند که در شرایط بیهوازی متان را بعنوان محصول حتمی متابولیسم تولید میکنند.آنها معمولاً در جاهای مرطوب مسئول تولید گاز متان هستند و در رودهٔ جانورانی مثل نشخوارکنندگان و انسانها مسئول تولید باد شکم هستندرشد و بقای آنها به طور مستقیم به فعالیت آنها با میکرو فلور بستگی دارد. رسوبات دریایی متانی کلا به جاهایی که از سولفات خالی شده‌اند، معمولاً زیر لایه‌های بالایی، محدود شده‌اند. بقیه اکسترمو فیل هستند و در محیطهای داغ مانند چشمه‌های آبگرم و نیز در کیلومترها زیر سطح زمین در سنگهای مذاب پوستهٔ زمین یافت شده‌اند. متانوژنها بیهوازی اند و همینطور نمیتوانند عملکردی در شرایط هوازی داشته باشند ولی میتوانند تنش اکسیژنی را برای مدت طولانی تحمل کنند. موردی استثنا وجود دارد بنام Methanosarcina barkeri که دارای آنزیم سوپراکسید دیس موتاز است و میتواند تنش اکسیژن را برای مدت بیشتری تحمل کند. برخی که هیدروژن تروفیک نامیده میشوند از CO۲ بعنوان منبع کربن و از H۲ بعنوان احیا کننده استفاده میکنند. مقداری از CO۲ با H۲ برای تولید متان وارد واکنش می‌شود که یک گرادیان الکتروشیمیایی در عرض غشا ایجاد می‌شود که ATP را در جهت شیمیو اسمزی مصرف میکند. برخلاف اینها، گیاهان و جلبکها از آب بعنوان احیا کننده استفاده میکنند. متانوژن و اطراف: اکثر متان بیوژنیک دریایی نتیجهٔ احیای CO۲ است و اندکی نیز از استات است.آرکه‌های کاتابولیز کننده از استات، استوتروفیک یا استیک لاستیک نامیده میشوند. آرکه‌های متیلوتروفیک از ترکیبات متیل دار مثل متیل آمین‌ها، متانول و نیز متان تیول استفاده میکنند. متانوژنها نقش اکولوژیکی حیاتی در محیطهای بیهوازی با زدودن هیدروژن اضافی و محصولات تخمیری که توسط فرمهای دیگر تنفس بیهوازی تولید شده‌اند ایفا میکند. متانوژنها بطور مشخص در محیطهایی که در آن بقیهٔ گیرنده‌های الکترون(مثل نیترات، اکسیژن، سولفات و آهن سه ظرفیتی)موجود نباشند، رونق میابند. در سنگهای عمیق هیدروژن مورد نیازشان را از آب تجزیه شدهٔ رادیواکتیو و گرم فراهم میکنند. متانوژنها در محیطهای افراطی بر روی زمین یافت میشوند از محیطهای گرم و خشک در صحرا تا در زیر کیلومترها یخ در گرینلند. اکثر متانوژنها تولید کننده‌های اتوتروف هستند اما آنهایی که از استات استفاده میکنند در جایگاه شیموهترتروف‌ها هستند. میکروبهای زنده‌ای که متان میساختند در هستهٔ نمونه‌های یخی از سه کیلومتری زیر گرینلند بوسیلهٔ تحقیقاتی از University of California, Berkeley یافت شد.


لینه
۱۷۳۵[۵]
دوسلسله‌ای
ارنست هکل
۱۸۶۶[۶]
سه‌سلسله‌ای
چاتون
۱۹۲۵[۷][۸]
دوقلمرویی
کوپلند
۱۹۳۸[۹][۱۰]
چهارسلسله‌ای
ویتکر
۱۹۶۹[۱۱]
پنج‌سلسله‌ای
وسس و دیگران
۱۹۷۷[۱۲][۱۳]
شش‌سلسله‌ای
وسس و دیگران
۱۹۹۰[۱۴]
سه‌فرمانرویی
کاوالیر اسمیت
۲۰۰۴[۱۵]
شش‌سلسله‌ای
(در نظر گرفته نشده) آغازیان پروکاریوت مونرا مونرا باکتری‌ها باکتری‌ها باکتری‌ها
باستانیان باستانیان
یوکاریوت آغازیان آغازیان آغازیان یوکاریوت تک‌یاختگان
کرومیستا
گیاهان گیاهان گیاهان گیاهان گیاهان گیاهان
آغازیان قارچ قارچ قارچ
جانوران جانوران جانوران جانوران جانوران جانوران


منابع و پانویس‌ها[ویرایش]

  • Wikipedia contributors, «Archaea,» Wikipedia, The Free Encyclopedia, (accessed November ۱۵, ۲۰۰۸).
  1. Paleoarchean
  2. Neomura
  3. Carl Woese
  4. دانش - زندگی زیر ژرفنا، در: روزنامهٔ کارگزاران، شماره ۵۱۴، چهارشنبه، ۲۲ خرداد، ۱۳۸، بازدید: نوامبر ۲۰۰۸.
  5. C. Linnaeus (1735). Systemae Naturae, sive regna tria naturae, systematics proposita per classes, ordines, genera & species. 
  6. E. Haeckel (1866). Generelle Morphologie der Organismen. Reimer, Berlin. 
  7. É. Chatton (1925). "Pansporella perplexa. Réflexions sur la biologie et la phylogénie des protozoaires". Ann. Sci. Nat. Zool 10-VII: 1–84. 
  8. É. Chatton (1937). Titres et Travaux Scientifiques (1906–1937). Sette, Sottano, Italy. 
  9. H. Copeland (1938). "The kingdoms of organisms". Quarterly review of biology 13: 383–420. DOI:10.1086/394568. 
  10. H. F. Copeland (1956). The Classification of Lower Organisms. Palo Alto: Pacific Books. 
  11. Whittaker RH (January 1969). "New concepts of kingdoms of organisms". Science 163 (3863): 150–60. DOI:10.1126/science.163.3863.150. PMID 5762760. 
  12. C. R. Woese, W. E. Balch, L. J. Magrum, G. E. Fox and R. S. Wolfe (August 1977). "An ancient divergence among the bacteria". Journal of Molecular Evolution 9 (4): 305–311. DOI:10.1007/BF01796092. PMID 408502. 
  13. Woese CR, Fox GE (November 1977). "Phylogenetic structure of the prokaryotic domain: the primary kingdoms". Proc. Natl. Acad. Sci. U.S.A. 74 (11): 5088–90. DOI:10.1073/pnas.74.11.5088. PMC 432104. PMID 270744. 
  14. Woese C, Kandler O, Wheelis M (1990). "Towards a natural system of organisms: proposal for the domains Archaea, Bacteria, and Eucarya.". Proc Natl Acad Sci U S A 87 (12): 4576–9. Bibcode 1990PNAS...87.4576W. DOI:10.1073/pnas.87.12.4576. PMC 54159. PMID 2112744. 
  15. Cavalier-Smith, T. (2004), "Only six kingdoms of life", Proc. R. Soc. Lond. B 271: 1251–62, doi:10.1098/rspb.2004.2705, PMC 1691724, PMID 15306349, retrieved 2010-04-29 
جستجو در ویکی‌انبار در ویکی‌انبار پرونده‌هایی دربارهٔ باستانیان موجود است.

Archaea
Temporal range: Paleoarchean or perhaps Eoarchean – Recent
Halobacteria sp. strain NRC-1,
each cell about 5 μm long
Scientific classification
Domain: Archaea
Woese, Kandler & Wheelis, 1990
Kingdoms and phyla

Crenarchaeota
Euryarchaeota
Korarchaeota
Nanoarchaeota
Thaumarchaeota

The Archaea (Listeni/ɑrˈkə/ or /ɑrˈkə/; singular archaeon) are a domain or kingdom of single-celled microorganisms. These microbes are prokaryotes, meaning they have no cell nucleus or any other membrane-bound organelles in their cells.

Archaea were initially classified as bacteria, receiving the name archaebacteria (or Kingdom Monera), but this classification is outdated.[1] Archaeal cells have unique properties separating them from the other two domains of life: Bacteria and Eukaryota. The Archaea are further divided into four recognized phyla. Classification is difficult, because the majority have not been studied in the laboratory and have only been detected by analysis of their nucleic acids in samples from their environment.

Archaea and bacteria are similar in size and shape, although a few archaea have very strange shapes, such as the flat and square-shaped cells of Haloquadratum walsbyi. Despite this visual similarity to bacteria, archaea possess genes and several metabolic pathways that are more closely related to those of eukaryotes, notably the enzymes involved in transcription and translation. Other aspects of archaeal biochemistry are unique, such as their reliance on ether lipids in their cell membranes. Archaea use more energy sources than eukaryotes: ranging from organic compounds such as sugars, to ammonia, metal ions or even hydrogen gas. Salt-tolerant archaea (the Haloarchaea) use sunlight as an energy source, and other species of archaea fix carbon; however, unlike plants and cyanobacteria, no species of archaea does both. Archaea reproduce asexually by binary fission, fragmentation, or budding; unlike bacteria and eukaryotes, no species form spores.

Archaea were initially viewed as extremophiles living in harsh environments, such as hot springs and salt lakes, but they have since been found in a broad range of habitats, including soils, oceans, marshlands and the human colon and navel.[2] Archaea are particularly numerous in the oceans, and the archaea in plankton may be one of the most abundant groups of organisms on the planet. Archaea are a major part of Earth's life and may play roles in both the carbon cycle and the nitrogen cycle. No clear examples of archaeal pathogens or parasites are known, but they are often mutualists or commensals. One example is the methanogens that inhabit the human gut and the ruminant gut, where their vast numbers aid digestion. Methanogens are used in biogas production and sewage treatment, and enzymes from extremophile archaea that can endure high temperatures and organic solvents are exploited in biotechnology.

Classification

New domain

For much of the 20th century, prokaryotes were regarded as a single group of organisms and classified based on their biochemistry, morphology and metabolism. For example, microbiologists tried to classify microorganisms based on the structures of their cell walls, their shapes, and the substances they consume.[3] However, a new approach was proposed in 1965,[4] using the sequences of the genes in these organisms to work out how different prokaryotes are related to each other. This approach, known as phylogenetics, is the main method used today.

Archaea were first found in extreme environments, such as volcanic hot springs. Pictured here is Grand Prismatic Spring of Yellowstone National Park.

Archaea were first classified as a separate group of prokaryotes in 1977 by Carl Woese and George E. Fox in phylogenetic trees based on the sequences of ribosomal RNA (rRNA) genes.[5] These two groups were originally named the Archaebacteria and Eubacteria and treated as kingdoms or subkingdoms, which Woese and Fox termed Urkingdoms. Woese argued that this group of prokaryotes is a fundamentally different sort of life. To emphasize this difference, these two domains were later renamed Archaea and Bacteria.[6] The word archaea comes from the Ancient Greek ἀρχαῖα, meaning "ancient things".[7] The first representatives of the domain Archaea were methanogens. For a long time archaea were seen as extremophiles that only exist in extreme habitats such as hot springs and salt lakes. However, by the end of the 20th century, archaea had been identified in non-extreme environments as well. Today they are known to be a large and diverse group of organisms that are widely distributed in nature and are common in all habitats.[8] This new appreciation of the importance and ubiquity of archaea came from using polymerase chain reaction (PCR) to detect prokaryotes from environmental samples (such as water or soil) by multiplying their ribosomal genes. This allows the detection and identification of organisms that have not been cultured in the laboratory.[9][10]

Current classification

The classification of archaea, and of prokaryotes in general, is a rapidly moving and contentious field. Current classification systems aim to organize archaea into groups of organisms that share structural features and common ancestors.[11] These classifications rely heavily on the use of the sequence of ribosomal RNA genes to reveal relationships between organisms (molecular phylogenetics).[12] Most of the culturable and well-investigated species of archaea are members of two main phyla, the Euryarchaeota and Crenarchaeota. Other groups have been tentatively created. For example, the peculiar species Nanoarchaeum equitans, which was discovered in 2003, has been given its own phylum, the Nanoarchaeota.[13] A new phylum Korarchaeota has also been proposed. It contains a small group of unusual thermophilic species that shares features of both of the main phyla, but is most closely related to the Crenarchaeota.[14][15] Other recently detected species of archaea are only distantly related to any of these groups, such as the Archaeal Richmond Mine acidophilic nanoorganisms (ARMAN), which were discovered in 2006[16] and are some of the smallest organisms known.[17]

A superphylum - TACK - has been proposed that includes the Aigarchaeota, Crenarchaeota, Korarchaeota and Thaumarchaeota.[18] This superphylum may be related to the origin of eukaryotes.

The ARMAN are a new group of archaea recently discovered in acid mine drainage.

Species

The classification of archaea into species is also controversial. Biology defines a species as a group of related organisms. The familiar exclusive breeding criterion (organisms that can breed with each other but not with others) is of no help because archaea reproduce asexually.[19]

Archaea show high levels of horizontal gene transfer between lineages. Some researchers suggest that individuals can be grouped into species-like populations given highly similar genomes and infrequent gene transfer to/from cells with less-related genomes, as in the genus Ferroplasma.[20] On the other hand, studies in Halorubrum found significant genetic transfer to/from less-related populations, limiting the criterion's applicability.[21] A second concern is to what extent such species designations have practical meaning.[22]

Current knowledge on genetic diversity is fragmentary and the total number of archaeal species cannot be estimated with any accuracy.[12] Estimates of the number of phyla range from 18 to 23, of which only 8 have representatives that have been cultured and studied directly. Many of these hypothesized groups are known from a single rRNA sequence, indicating that the diversity among these organisms remains obscure.[23] The Bacteria also contain many uncultured microbes with similar implications for characterization.[24]

Origin and evolution

Euryarchaeota Nanoarchaeota Crenarchaeota Protozoa Algae Plantae Slime molds Animal Fungus Gram-positive bacteria Chlamydiae Chloroflexi Actinobacteria Planctomycetes Spirochaetes Fusobacteria Cyanobacteria Thermophiles Acidobacteria Proteobacteria
Phylogenetic tree showing the relationship between the Archaea and other domains of life. Eukaryotes are colored red, archaea green and bacteria blue. Adapted from Ciccarelli et al. (2006)[25]

Scientific evidence suggests that life began on Earth at least 3.5 billion years ago.[26][27] The earliest evidences for life on Earth are graphite found to be biogenic in 3.7 billion-year-old metasedimentary rocks discovered in Western Greenland[28] and microbial mat fossils found in 3.48 billion-year-old sandstone discovered in Western Australia.[29][30]

Although probable prokaryotic cell fossils date to almost 3.5 billion years ago, most prokaryotes do not have distinctive morphologies and fossil shapes cannot be used to identify them as Archaea.[31] Instead, chemical fossils of unique lipids are more informative because such compounds do not occur in other organisms.[32] Some publications suggest that archaeal or eukaryotic lipid remains are present in shales dating from 2.7 billion years ago;[33] such data have since been questioned.[34] Such lipids have also been detected in even older rocks from west Greenland. The oldest such traces come from the Isua district, which include Earth's oldest sediments, formed 3.8 billion years ago.[35] The archaeal lineage may be the most ancient that exists on Earth.[36]

Woese argued that the bacteria, archaea, and eukaryotes represent separate lines of descent that diverged early on from an ancestral colony of organisms.[37][38] One possibility[38][39] is that this occurred before the evolution of cells, when the lack of a typical cell membrane allowed unrestricted lateral gene transfer, and that the common ancestors of the three domains arose by fixation of specific subsets of genes.[38][39] It is possible that the last common ancestor of the bacteria and archaea was a thermophile, which raises the possibility that lower temperatures are "extreme environments" in archaeal terms, and organisms that live in cooler environments appeared only later.[40] Since the Archaea and Bacteria are no more related to each other than they are to eukaryotes, the term prokaryote's only surviving meaning is "not a eukaryote", limiting its value.[41]

Comparison to other domains

The following table describes some major characteristics that are generally shared by Archaea with the other two domains or with neither, to illustrate the relationships to each.[42] Many of these characteristics are also discussed below.

Shared with Bacteria Shared with Eukarya Unique to Archaea
No nucleus or membrane-bound organelles No peptidoglycan Cell wall structure (for example, some archaeal cell walls contain pseudomurein)
Circular genome DNA associated with histones[43][44] Cell membrane containing ether-linked lipids
Genes grouped in operons Translation initiated with methionine Flagellin protein structure[45]
No introns or RNA processing Similar RNA polymerase, promoters, other transcriptional machinery[45][46][47] Ribosomal structure (characteristics shared with both Bacteria and Eukarya)
Polycistronic mRNA Similar DNA replication and repair[48] tRNA sequence and metabolism[45][49]
Cellular size (>100-fold smaller than eukaryotes) Similar ATPase (Type V) No fatty acid synthetase enzyme[45]

Relationship to other prokaryotes

The relationship between the three domains is of central importance for understanding the origin of life. Most of the metabolic pathways, which comprise the majority of an organism's genes, are common between Archaea and Bacteria, while most genes involved in genome expression are common between Archaea and Eukarya.[50] Within prokaryotes, archaeal cell structure is most similar to that of Gram-positive bacteria, largely because both have a single lipid bilayer[51] and usually contain a thick sacculus of varying chemical composition.[52] In phylogenetic trees based upon different gene/protein sequences of prokaryotic homologs, the archaeal homologs are more closely related to those of Gram-positive bacteria.[51] Archaea and Gram-positive bacteria also share conserved indels in a number of important proteins, such as Hsp70 and glutamine synthetase I.[51][53][54]

R.S. Gupta has proposed that the archaea evolved from Gram-positive bacteria in response to antibiotic selection pressure.[51][53][55] This is suggested by the observation that archaea are resistant to a wide variety of antibiotics that are primarily produced by Gram-positive bacteria,[51][53] and that these antibiotics primarily act on the genes that distinguish archaea from bacteria. His proposal is that the selective pressure towards resistance generated by the Gram-positive antibiotics was eventually sufficient to cause extensive changes in many of the antibiotics' target genes, and that these strains represented the common ancestors of present-day Archaea.[55] The evolution of Archaea in response to antibiotic selection, or any other competitive selective pressure, could also explain their adaptation to extreme environments (such as high temperature or acidity) as the result of a search for unoccupied niches to escape from antibiotic-producing organisms;[55][56] Cavalier-Smith has made a similar suggestion.[57] Gupta's proposal is also supported by other work investigating protein structural relationships[58] and studies that suggest that Gram-positive bacteria may constitute the earliest branching lineages within the prokaryotes.[59]

Relation to eukaryotes

The evolutionary relationship between archaea and eukaryotes remains unclear. Aside from the similarities in cell structure and function that are discussed below, many genetic trees group the two.

Complicating factors include claims that the relationship between eukaryotes and the archaeal phylum Crenarchaeota is closer than the relationship between the Euryarchaeota and the phylum Crenarchaeota[60] and the presence of archaea-like genes in certain bacteria, such as Thermotoga maritima, from horizontal gene transfer.[61] The standard hypothesis states that the ancestor of the eukaryotes diverged early from the Archaea,[62][63] and that eukaryotes arose through fusion of an archaean and eubacterium, which became the nucleus and cytoplasm; this explains various genetic similarities but runs into difficulties explaining cell structure.[64] An alternative hypothesis, the eocyte hypothesis, posits that Eukaryota emerged relatively late from the Archaea.[65]

Morphology

The sizes of prokaryotic cells relative to other cells and biomolecules (logarithmic scale)

Individual archaea range from 0.1 micrometers (μm) to over 15 μm in diameter, and occur in various shapes, commonly as spheres, rods, spirals or plates.[66] Other morphologies in the Crenarchaeota include irregularly shaped lobed cells in Sulfolobus, needle-like filaments that are less than half a micrometer in diameter in Thermofilum, and almost perfectly rectangular rods in Thermoproteus and Pyrobaculum.[67] Haloquadratum walsbyi are flat, square archaea that live in hypersaline pools.[68] These unusual shapes are probably maintained both by their cell walls and a prokaryotic cytoskeleton. Proteins related to the cytoskeleton components of other organisms exist in archaea,[69] and filaments form within their cells,[70] but in contrast to other organisms, these cellular structures are poorly understood.[71] In Thermoplasma and Ferroplasma the lack of a cell wall means that the cells have irregular shapes, and can resemble amoebae.[72]

Some species form aggregates or filaments of cells up to 200 μm long.[66] These organisms can be prominent in biofilms.[73] Notably, aggregates of Thermococcus coalescens cells fuse together in culture, forming single giant cells.[74] Archaea in the genus Pyrodictium produce an elaborate multicell colony involving arrays of long, thin hollow tubes called cannulae that stick out from the cells' surfaces and connect them into a dense bush-like agglomeration.[75] The function of these cannulae is not settled, but they may allow communication or nutrient exchange with neighbors.[76] Multi-species colonies exist, such as the "string-of-pearls" community that was discovered in 2001 in a German swamp. Round whitish colonies of a novel Euryarchaeota species are spaced along thin filaments that can range up to 15 centimetres (5.9 in) long; these filaments are made of a particular bacteria species.[77]

Structure, composition development, operation

Archaea and bacteria have generally similar cell structure, but cell composition and organization set the archaea apart. Like bacteria, archaea lack interior membranes and organelles.[41] Like bacteria, archaea cell membranes are usually bounded by a cell wall and they swim using one or more flagella.[78] Structurally, archaea are most similar to Gram-positive bacteria. Most have a single plasma membrane and cell wall, and lack a periplasmic space; the exception to this general rule is Ignicoccus, which possess a particularly large periplasm that contains membrane-bound vesicles and is enclosed by an outer membrane.[79]

Membranes

Membrane structures. Top, an archaeal phospholipid: 1, isoprene chains; 2, ether linkages; 3, L-glycerol moiety; 4, phosphate group. Middle, a bacterial or eukaryotic phospholipid: 5, fatty acid chains; 6, ester linkages; 7, D-glycerol moiety; 8, phosphate group. Bottom: 9, lipid bilayer of bacteria and eukaryotes; 10, lipid monolayer of some archaea.

Archaeal membranes are made of molecules that differ strongly from those in other life forms, showing that archaea are related only distantly to bacteria and eukaryotes.[80] In all organisms cell membranes are made of molecules known as phospholipids. These molecules possess both a polar part that dissolves in water (the phosphate "head"), and a "greasy" non-polar part that does not (the lipid tail). These dissimilar parts are connected by a glycerol moiety. In water, phospholipids cluster, with the heads facing the water and the tails facing away from it. The major structure in cell membranes is a double layer of these phospholipids, which is called a lipid bilayer.

These phospholipids are unusual in four ways:

  • Bacteria and eukaryotes have membranes composed mainly of glycerol-ester lipids, whereas archaea have membranes composed of glycerol-ether lipids.[81] The difference is the type of bond that joins the lipids to the glycerol moiety; the two types are shown in yellow in the figure at the right. In ester lipids this is an ester bond, whereas in ether lipids this is an ether bond. Ether bonds are chemically more resistant than ester bonds. This stability might help archaea to survive extreme temperatures and very acidic or alkaline environments.[82] Bacteria and eukaryotes do contain some ether lipids, but in contrast to archaea these lipids are not a major part of their membranes.
  • The stereochemistry of the glycerol moiety is the reverse of that found in other organisms. The glycerol moiety can occur in two forms that are mirror images of one another, called the right-handed and left-handed forms; in chemistry these are called enantiomers. Just as a right hand does not fit easily into a left-handed glove, a right-handed phospholipid generally cannot be used or made by enzymes adapted for the left-handed form. This suggests that archaea use entirely different enzymes for synthesizing phospholipids than do bacteria and eukaryotes. Such enzymes developed very early in life's history, suggesting an early split from the other two domains.[80]
  • Archaeal lipid tails are chemically different from other organisms. Archaeal lipids are based upon the isoprenoid sidechain and are long chains with multiple side-branches and sometimes even cyclopropane or cyclohexane rings.[83] This is in contrast to the fatty acids found in other organisms' membranes, which have straight chains with no branches or rings. Although isoprenoids play an important role in the biochemistry of many organisms, only the archaea use them to make phospholipids. These branched chains may help prevent archaeal membranes from leaking at high temperatures.[84]
  • In some archaea the lipid bilayer is replaced by a monolayer. In effect, the archaea fuse the tails of two independent phospholipid molecules into a single molecule with two polar heads (a bolaamphiphile); this fusion may make their membranes more rigid and better able to resist harsh environments.[85] For example, the lipids in Ferroplasma are of this type, which is thought to aid this organism's survival in its highly acidic habitat.[86]

Wall and flagella

Most archaea (but not Thermoplasma and Ferroplasma) possess a cell wall.[72] In most archaea the wall is assembled from surface-layer proteins, which form an S-layer.[87] An S-layer is a rigid array of protein molecules that cover the outside of the cell (like chain mail).[88] This layer provides both chemical and physical protection, and can prevent macromolecules from contacting the cell membrane.[89] Unlike bacteria, archaea lack peptidoglycan in their cell walls.[90] Methanobacteriales do have cell walls containing pseudopeptidoglycan, which resembles eubacterial peptidoglycan in morphology, function, and physical structure, but pseudopeptidoglycan is distinct in chemical structure; it lacks D-amino acids and N-acetylmuramic acid.[89]

Archaea flagella operate like bacterial flagella—their long stalks are driven by rotatory motors at the base. These motors are powered by the proton gradient across the membrane. However, archaeal flagella are notably different in composition and development.[78] The two types of flagella evolved from different ancestors. The bacterial flagellum shares a common ancestor with the type III secretion system,[91][92] while archaeal flagella appear to have evolved from bacterial type IV pili.[93] In contrast to the bacterial flagellum, which is hollow and is assembled by subunits moving up the central pore to the tip of the flagella, archaeal flagella are synthesized by adding subunits at the base.[94]

Metabolism

Archaea exhibit a great variety of chemical reactions in their metabolism and use many sources of energy. These reactions are classified into nutritional groups, depending on energy and carbon sources. Some archaea obtain energy from inorganic compounds such as sulfur or ammonia (they are lithotrophs). These include nitrifiers, methanogens and anaerobic methane oxidisers.[95] In these reactions one compound passes electrons to another (in a redox reaction), releasing energy to fuel the cell's activities. One compound acts as an electron donor and one as an electron acceptor. The energy released generates adenosine triphosphate (ATP) through chemiosmosis, in the same basic process that happens in the mitochondrion of eukaryotic cells.[96]

Other groups of archaea use sunlight as a source of energy (they are phototrophs). However, oxygen–generating photosynthesis does not occur in any of these organisms.[96] Many basic metabolic pathways are shared between all forms of life; for example, archaea use a modified form of glycolysis (the Entner–Doudoroff pathway) and either a complete or partial citric acid cycle.[45] These similarities to other organisms probably reflect both early origins in the history of life and their high level of efficiency.[97]

Nutritional types in archaeal metabolism
Nutritional type Source of energy Source of carbon Examples
 Phototrophs   Sunlight   Organic compounds   Halobacteria 
 Lithotrophs  Inorganic compounds  Organic compounds or carbon fixation  Ferroglobus, Methanobacteria or Pyrolobus 
 Organotrophs  Organic compounds   Organic compounds or carbon fixation   Pyrococcus, Sulfolobus or Methanosarcinales 

Some Euryarchaeota are methanogens living in anaerobic environments such as swamps. This form of metabolism evolved early, and it is even possible that the first free-living organism was a methanogen.[98] A common reaction involves the use of carbon dioxide as an electron acceptor to oxidize hydrogen. Methanogenesis involves a range of coenzymes that are unique to these archaea, such as coenzyme M and methanofuran.[99] Other organic compounds such as alcohols, acetic acid or formic acid are used as alternative electron acceptors by methanogens. These reactions are common in gut-dwelling archaea. Acetic acid is also broken down into methane and carbon dioxide directly, by acetotrophic archaea. These acetotrophs are archaea in the order Methanosarcinales, and are a major part of the communities of microorganisms that produce biogas.[100]

Bacteriorhodopsin from Halobacterium salinarum. The retinol cofactor and residues involved in proton transfer are shown as ball-and-stick models.[101]

Other archaea use CO
2
in the atmosphere as a source of carbon, in a process called carbon fixation (they are autotrophs). This process involves either a highly modified form of the Calvin cycle[102] or a recently discovered metabolic pathway called the 3-hydroxypropionate/4-hydroxybutyrate cycle.[103] The Crenarchaeota also use the reverse Krebs cycle while the Euryarchaeota also use the reductive acetyl-CoA pathway.[104] Carbon–fixation is powered by inorganic energy sources. No known archaea carry out photosynthesis.[105] Archaeal energy sources are extremely diverse, and range from the oxidation of ammonia by the Nitrosopumilales[106][107] to the oxidation of hydrogen sulfide or elemental sulfur by species of Sulfolobus, using either oxygen or metal ions as electron acceptors.[96]

Phototrophic archaea use light to produce chemical energy in the form of ATP. In the Halobacteria, light-activated ion pumps like bacteriorhodopsin and halorhodopsin generate ion gradients by pumping ions out of the cell across the plasma membrane. The energy stored in these electrochemical gradients is then converted into ATP by ATP synthase.[66] This process is a form of photophosphorylation. The ability of these light-driven pumps to move ions across membranes depends on light-driven changes in the structure of a retinol cofactor buried in the center of the protein.[108]

Genetics

Archaea usually have a single circular chromosome,[109] the size of which may be as great as 5,751,492 base pairs in Methanosarcina acetivorans,[110] the largest known archaeal genome. One-tenth of this size is the tiny 490,885 base-pair genome of Nanoarchaeum equitans, the smallest archaeal genome known; it is estimated to contain only 537 protein-encoding genes.[111] Smaller independent pieces of DNA, called plasmids, are also found in archaea. Plasmids may be transferred between cells by physical contact, in a process that may be similar to bacterial conjugation.[112][113]

Sulfolobus infected with the DNA virus STSV1.[114] Bar is 1 micrometer.

Archaea can be infected by double-stranded DNA viruses that are unrelated to any other form of virus and have a variety of unusual shapes, including bottles, hooked rods, or teardrops.[115] These viruses have been studied in most detail in thermophilics, particularly the orders Sulfolobales and Thermoproteales.[116] Two groups of single-stranded DNA viruses that infect archaea have been recently isolated. One group is exemplified by the Halorubrum pleomorphic virus 1 ("Pleolipoviridae") infecting halophilic archaea[117] and the other one by the Aeropyrum coil-shaped virus ("Spiraviridae") infecting a hyperthermophilic (optimal growth at 90–95 °C) host.[118] Notably, the latter virus has the largest currently reported ssDNA genome. Defenses against these viruses may involve RNA interference from repetitive DNA sequences that are related to the genes of the viruses.[119][120]

Archaea are genetically distinct from bacteria and eukaryotes, with up to 15% of the proteins encoded by any one archaeal genome being unique to the domain, although most of these unique genes have no known function.[121] Of the remainder of the unique proteins that have an identified function, most belong to the Euryarchaea and are involved in methanogenesis. The proteins that archaea, bacteria and eukaryotes share form a common core of cell function, relating mostly to transcription, translation, and nucleotide metabolism.[122] Other characteristic archaeal features are the organization of genes of related function—such as enzymes that catalyze steps in the same metabolic pathway into novel operons, and large differences in tRNA genes and their aminoacyl tRNA synthetases.[122]

Transcription and translation in archaea resemble these processes in eukaryotes more than in bacteria, with the archaeal RNA polymerase and ribosomes being very close to their equivalents in eukaryotes.[109] Although archaea only have one type of RNA polymerase, its structure and function in transcription seems to be close to that of the eukaryotic RNA polymerase II, with similar protein assemblies (the general transcription factors) directing the binding of the RNA polymerase to a gene's promoter.[123] However, other archaeal transcription factors are closer to those found in bacteria.[124] Post-transcriptional modification is simpler than in eukaryotes, since most archaeal genes lack introns, although there are many introns in their transfer RNA and ribosomal RNA genes,[125] and introns may occur in a few protein-encoding genes.[126][127]

Gene transfer and genetic exchange

Halobacterium volcanii, an extreme halophilic archaeon, forms cytoplasmic bridges between cells that appear to be used for transfer of DNA from one cell to another in either direction.[128]

When the hyperthermophilic archaea Sulfolobus solfataricus[129] and Sulfolobus acidocaldarius[130] are exposed to the DNA damaging agents UV irradiation, bleomycin or mitomycin C, species-specific cellular aggregation is induced. Aggregation in S. solfataricus could not be induced by other physical stressors, such as pH or temperature shift,[129] suggesting that aggregation is induced specifically by DNA damage. Ajon et al.[130] showed that UV-induced cellular aggregation mediates chromosomal marker exchange with high frequency in S. acidocaldarius. Recombination rates exceeded those of uninduced cultures by up to three orders of magnitude. Frols et al.[129][131] and Ajon et al.[130] hypothesized that cellular aggregation enhances species specific DNA transfer between Sulfolobus cells in order to provide increased repair of damaged DNA by means of homologous recombination. This response may be a primitive form of sexual interaction similar to the more well-studied bacterial transformation systems that are also associated with species specific DNA transfer between cells leading to homologous recombinational repair of DNA damage.[132]

Reproduction

Archaea reproduce asexually by binary or multiple fission, fragmentation, or budding; meiosis does not occur, so if a species of archaea exists in more than one form, all have the same genetic material.[66] Cell division is controlled in a cell cycle; after the cell's chromosome is replicated and the two daughter chromosomes separate, the cell divides.[133] Details have only been investigated in the genus Sulfolobus, but that cycle has characteristics that are similar to both bacterial and eukaryotic systems. The chromosomes replicate from multiple starting-points (origins of replication) using DNA polymerases that resemble the equivalent eukaryotic enzymes.[134] However, the proteins that direct cell division, such as the protein FtsZ, which forms a contracting ring around the cell, and the components of the septum that is constructed across the center of the cell, are similar to their bacterial equivalents.[133]

Both bacteria and eukaryotes, but not archaea, make spores.[135] Some species of Haloarchaea undergo phenotypic switching and grow as several different cell types, including thick-walled structures that are resistant to osmotic shock and allow the archaea to survive in water at low salt concentrations, but these are not reproductive structures and may instead help them reach new habitats.[136]

Ecology

Habitats

Archaea exist in a broad range of habitats, and as a major part of global ecosystems,[8] may contribute up to 20% of earth's biomass.[137] The first-discovered archaeans were extremophiles.[95] Indeed, some archaea survive high temperatures, often above 100 °C (212 °F), as found in geysers, black smokers, and oil wells. Other common habitats include very cold habitats and highly saline, acidic, or alkaline water. However, archaea include mesophiles that grow in mild conditions, in marshland, sewage, the oceans, and soils.[8]

Image of plankton (light green) in the oceans; archaea form a major part of oceanic life.

Extremophile archaea are members of four main physiological groups. These are the halophiles, thermophiles, alkaliphiles, and acidophiles.[138] These groups are not comprehensive or phylum-specific, nor are they mutually exclusive, since some archaea belong to several groups. Nonetheless, they are a useful starting point for classification.

Halophiles, including the genus Halobacterium, live in extremely saline environments such as salt lakes and outnumber their bacterial counterparts at salinities greater than 20–25%.[95] Thermophiles grow best at temperatures above 45 °C (113 °F), in places such as hot springs; hyperthermophilic archaea grow optimally at temperatures greater than 80 °C (176 °F).[139] The archaeal Methanopyrus kandleri Strain 116 can even reproduce at 122 °C (252 °F), the highest recorded temperature of any organism.[140]

Other archaea exist in very acidic or alkaline conditions.[138] For example, one of the most extreme archaean acidophiles is Picrophilus torridus, which grows at pH 0, which is equivalent to thriving in 1.2 molar sulfuric acid.[141]

This resistance to extreme environments has made archaea the focus of speculation about the possible properties of extraterrestrial life.[142] Some extremophile habitats are not dissimilar to those on Mars,[143] leading to the suggestion that viable microbes could be transferred between planets in meteorites.[144]

Recently, several studies have shown that archaea exist not only in mesophilic and thermophilic environments but are also present, sometimes in high numbers, at low temperatures as well. For example, archaea are common in cold oceanic environments such as polar seas.[145] Even more significant are the large numbers of archaea found throughout the world's oceans in non-extreme habitats among the plankton community (as part of the picoplankton).[146] Although these archaea can be present in extremely high numbers (up to 40% of the microbial biomass), almost none of these species have been isolated and studied in pure culture.[147] Consequently, our understanding of the role of archaea in ocean ecology is rudimentary, so their full influence on global biogeochemical cycles remains largely unexplored.[148] Some marine Crenarchaeota are capable of nitrification, suggesting these organisms may affect the oceanic nitrogen cycle,[149] although these oceanic Crenarchaeota may also use other sources of energy.[150] Vast numbers of archaea are also found in the sediments that cover the sea floor, with these organisms making up the majority of living cells at depths over 1 meter below the ocean bottom.[151][152]

Role in chemical cycling

Archaea recycle elements such as carbon, nitrogen and sulfur through their various habitats. Although these activities are vital for normal ecosystem function, archaea can also contribute to human-made changes, and even cause pollution.

Archaea carry out many steps in the nitrogen cycle. This includes both reactions that remove nitrogen from ecosystems, such as nitrate-based respiration and denitrification, as well as processes that introduce nitrogen, such as nitrate assimilation and nitrogen fixation.[153][154] Archaean involvement in ammonia oxidation reactions was recently discovered. These reactions are particularly important in the oceans.[155][156] The archaea also appear to be crucial for ammonia oxidation in soils. They produce nitrite, which other microbes then oxidize to nitrate. Plants and other organisms consume the latter.[157]

In the sulfur cycle, archaea that grow by oxidizing sulfur compounds release this element from rocks, making it available to other organisms. However, the archaea that do this, such as Sulfolobus, produce sulfuric acid as a waste product, and the growth of these organisms in abandoned mines can contribute to acid mine drainage and other environmental damage.[158]

In the carbon cycle, methanogen archaea remove hydrogen and are important in the decay of organic matter by the populations of microorganisms that act as decomposers in anaerobic ecosystems, such as sediments, marshes and sewage treatment works.[159]

Methanogens are the primary source of atmospheric methane, and are responsible for most of the world's yearly methane emissions.[160] As a consequence, these archaea contribute to global greenhouse gas emissions and global warming.

Global methane levels, have risen to 1800 ppb by 2011, an increase by a factor of 2.5 since pre-industrial times, from 722 ppb, the highest value in at least 800,000 years.[161] Methane has an anthropogenic global warming potential (AGWP) of 29, which means that it's 29 times stronger in heat-trapping, than carbon dioxide is, over a 100-year time scale.[162]

Interactions with other organisms

Methanogenic archaea form a symbiosis with termites.

The well-characterized interactions between archaea and other organisms are either mutual or commensal. There are no clear examples of known archaeal pathogens or parasites.[163][164] However, a relationship has been proposed between some species of methanogens and infections in the mouth,[165][166] and Nanoarchaeum equitans may be a parasite of another species of archaea, since it only survives and reproduces within the cells of the Crenarchaeon Ignicoccus hospitalis,[167] and appears to offer no benefit to its host.[168] In contrast, Archaeal Richmond Mine Acidophilic Nanoorganisms (ARMAN) occasionally connect with other archaeal cells in acid mine drainage biofilms.[169] The nature of this relationship is unknown. However, it is distinct from that of Nanarchaeaum–Ignicoccus in that the ultrasmall ARMAN cells are usually seen independent of the Thermoplasmatales cells.

Mutualism

One well-understood example of mutualism is the interaction between protozoa and methanogenic archaea in the digestive tracts of animals that digest cellulose, such as ruminants and termites.[170] In these anaerobic environments, protozoa break down plant cellulose to obtain energy. This process releases hydrogen as a waste product, but high levels of hydrogen reduce energy production. When methanogens convert hydrogen to methane, protozoa benefit from more energy.[171]

In anaerobic protozoa such as Plagiopyla frontata, archaea reside inside the protozoa and consume hydrogen produced in their hydrogenosomes.[172][173] Archaea also associate with larger organisms. For example, the marine archaean Cenarchaeum symbiosum lives within (is an endosymbiont of) the sponge Axinella mexicana.[174]

Commensalism

Archaea can also be commensals, benefiting from an association without helping or harming the other organism. For example, the methanogen Methanobrevibacter smithii is by far the most common archaean in the human flora, making up about one in ten of all the prokaryotes in the human gut.[175] In termites and in humans, these methanogens may in fact be mutualists, interacting with other microbes in the gut to aid digestion.[176] Archaean communities also associate with a range of other organisms, such as on the surface of corals,[177] and in the region of soil that surrounds plant roots (the rhizosphere).[178][179]

Significance in technology and industry

Extremophile archaea, particularly those resistant either to heat or to extremes of acidity and alkalinity, are a source of enzymes that function under these harsh conditions.[180][181] These enzymes have found many uses. For example, thermostable DNA polymerases, such as the Pfu DNA polymerase from Pyrococcus furiosus, revolutionized molecular biology by allowing the polymerase chain reaction to be used in research as a simple and rapid technique for cloning DNA. In industry, amylases, galactosidases and pullulanases in other species of Pyrococcus that function at over 100 °C (212 °F) allow food processing at high temperatures, such as the production of low lactose milk and whey.[182] Enzymes from these thermophilic archaea also tend to be very stable in organic solvents, allowing their use in environmentally friendly processes in green chemistry that synthesize organic compounds.[181] This stability makes them easier to use in structural biology. Consequently the counterparts of bacterial or eukaryotic enzymes from extremophile archaea are often used in structural studies.[183]

In contrast to the range of applications of archaean enzymes, the use of the organisms themselves in biotechnology is less developed. Methanogenic archaea are a vital part of sewage treatment, since they are part of the community of microorganisms that carry out anaerobic digestion and produce biogas.[184] In mineral processing, acidophilic archaea display promise for the extraction of metals from ores, including gold, cobalt and copper.[185]

Archaea host a new class of potentially useful antibiotics. A few of these archaeocins have been characterized, but hundreds more are believed to exist, especially within Haloarchaea and Sulfolobus.These compounds differ in structure from bacterial antibiotics, so they may have novel modes of action. In addition, they may allow the creation of new selectable markers for use in archaeal molecular biology.[186]

See also

References

  1. ^ Pace NR (May 2006). "Time for a change". Nature 441 (7091): 289. Bibcode:2006Natur.441..289P. doi:10.1038/441289a. PMID 16710401. 
  2. ^ Dunn, Rob. "After 2 Years Scientists Still Can't Solve Belly Button Mystery, Continue Navel-Gazing". Guest Blog. Scientific American. Retrieved 16 January 2013. 
  3. ^ Staley JT (2006). "The bacterial species dilemma and the genomic-phylogenetic species concept". Philosophical Transactions of the Royal Society B 361 (1475): 1899–909. doi:10.1098/rstb.2006.1914. PMC 1857736. PMID 17062409. 
  4. ^ Zuckerkandl E, Pauling L (1965). "Molecules as documents of evolutionary history". J. Theor. Biol. 8 (2): 357–66. doi:10.1016/0022-5193(65)90083-4. PMID 5876245. 
  5. ^ Woese C, Fox G (1977). "Phylogenetic structure of the prokaryotic domain: the primary kingdoms". Proceedings of the National Academy of Sciences of the United States of America 74 (11): 5088–90. Bibcode:1977PNAS...74.5088W. doi:10.1073/pnas.74.11.5088. PMC 432104. PMID 270744. 
  6. ^ >Woese CR, Kandler O, Wheelis ML (1990). "Towards a natural system of organisms: proposal for the domains Archaea, Bacteria, and Eucarya". Proceedings of the National Academy of Sciences of the United States of America 87 (12): 4576–9. Bibcode:1990PNAS...87.4576W. doi:10.1073/pnas.87.12.4576. PMC 54159. PMID 2112744. 
  7. ^ archaea. (2008). In Merriam-Webster Online Dictionary. Retrieved July 1, 2008, from http://www.merriam-webster.com/dictionary/archaea
  8. ^ a b c DeLong EF (1998). "Everything in moderation: archaea as 'non-extremophiles'". Current Opinion in Genetics & Development 8 (6): 649–54. doi:10.1016/S0959-437X(98)80032-4. PMID 9914204. 
  9. ^ Theron J, Cloete TE (2000). "Molecular techniques for determining microbial diversity and community structure in natural environments". Crit. Rev. Microbiol. 26 (1): 37–57. doi:10.1080/10408410091154174. PMID 10782339. 
  10. ^ Schmidt TM (2006). "The maturing of microbial ecology" (PDF). Int. Microbiol. 9 (3): 217–23. PMID 17061212. 
  11. ^ Gevers D, Dawyndt P, Vandamme P, et al. (2006). "Stepping stones towards a new prokaryotic taxonomy". Philosophical Transactions of the Royal Society B 361 (1475): 1911–6. doi:10.1098/rstb.2006.1915. PMC 1764938. PMID 17062410. 
  12. ^ a b Robertson CE, Harris JK, Spear JR, Pace NR (2005). "Phylogenetic diversity and ecology of environmental Archaea". Current Opinion in Microbiology 8 (6): 638–42. doi:10.1016/j.mib.2005.10.003. PMID 16236543. 
  13. ^ Huber H, Hohn MJ, Rachel R, Fuchs T, Wimmer VC, Stetter KO. (2002). "A new phylum of Archaea represented by a nanosized hyperthermophilic symbiont". Nature 417 (6884): 27–8. Bibcode:2002Natur.417...63H. doi:10.1038/417063a. PMID 11986665. 
  14. ^ Barns SM, Delwiche CF, Palmer JD, Pace NR (1996). "Perspectives on archaeal diversity, thermophily and monophyly from environmental rRNA sequences". Proceedings of the National Academy of Sciences of the United States of America 93 (17): 9188–93. Bibcode:1996PNAS...93.9188B. doi:10.1073/pnas.93.17.9188. PMC 38617. PMID 8799176. 
  15. ^ Elkins JG, Podar M, Graham DE, et al. (June 2008). "A korarchaeal genome reveals insights into the evolution of the Archaea". Proceedings of the National Academy of Sciences of the United States of America 105 (23): 8102–7. Bibcode:2008PNAS..105.8102E. doi:10.1073/pnas.0801980105. PMC 2430366. PMID 18535141. 
  16. ^ Baker, B.J., Tyson, G.W., Webb, R.I., Flanagan, J., Hugenholtz, P. and Banfield, J.F. (2006). "Lineages of acidophilic Archaea revealed by community genomic analysis. Science". Science 314 (6884): 1933–1935. Bibcode:2006Sci...314.1933B. doi:10.1126/science.1132690. PMID 17185602. 
  17. ^ Baker BJ, Comolli LR, Dick GJ, et al. (May 2010). "Enigmatic, ultrasmall, uncultivated Archaea". Proceedings of the National Academy of Sciences of the United States of America 107 (19): 8806–11. Bibcode:2010PNAS..107.8806B. doi:10.1073/pnas.0914470107. PMC 2889320. PMID 20421484. 
  18. ^ Guy, L; Ettema, TJ (19 December 2011). "The archaeal ‘TACK’ superphylum and the origin of eukaryotes.". Trends Microbiol. 19: 580–587. doi:10.1016/j.tim.2011.09.002. Retrieved 3 April 2014. 
  19. ^ de Queiroz K (2005). "Ernst Mayr and the modern concept of species". Proceedings of the National Academy of Sciences of the United States of America 102 (Suppl 1): 6600–7. Bibcode:2005PNAS..102.6600D. doi:10.1073/pnas.0502030102. PMC 1131873. PMID 15851674. 
  20. ^ Eppley JM, Tyson GW, Getz WM, Banfield JF (2007). "Genetic exchange across a species boundary in the archaeal genus ferroplasma". Genetics 177 (1): 407–16. doi:10.1534/genetics.107.072892. PMC 2013692. PMID 17603112. 
  21. ^ Papke RT, Zhaxybayeva O, Feil EJ, Sommerfeld K, Muise D, Doolittle WF (2007). "Searching for species in haloarchaea". Proceedings of the National Academy of Sciences of the United States of America 104 (35): 14092–7. Bibcode:2007PNAS..10414092P. doi:10.1073/pnas.0706358104. PMC 1955782. PMID 17715057. 
  22. ^ Kunin V, Goldovsky L, Darzentas N, Ouzounis CA (2005). "The net of life: reconstructing the microbial phylogenetic network". Genome Res. 15 (7): 954–9. doi:10.1101/gr.3666505. PMC 1172039. PMID 15965028. 
  23. ^ Hugenholtz P (2002). "Exploring prokaryotic diversity in the genomic era". Genome Biol. 3 (2): REVIEWS0003. doi:10.1186/gb-2002-3-2-reviews0003. PMC 139013. PMID 11864374. 
  24. ^ Rappé MS, Giovannoni SJ (2003). "The uncultured microbial majority". Annu. Rev. Microbiol. 57: 369–94. doi:10.1146/annurev.micro.57.030502.090759. PMID 14527284. 
  25. ^ Ciccarelli FD, Doerks T, von Mering C, Creevey CJ, Snel B, Bork P (2006). "Toward automatic reconstruction of a highly resolved tree of life". Science 311 (5765): 1283–7. Bibcode:2006Sci...311.1283C. doi:10.1126/science.1123061. PMID 16513982. 
  26. ^ de Duve, Christian (October 1995). "The Beginnings of Life on Earth". American Scientist. Retrieved 15 January 2014. 
  27. ^ Timmer, John (4 September 2012). "3.5 billion year old organic deposits show signs of life". Ars Technica. Retrieved 15 January 2014. 
  28. ^ Yoko Ohtomo, Takeshi Kakegawa, Akizumi Ishida, Toshiro Nagase, Minik T. Rosing (8 December 2013). "Evidence for biogenic graphite in early Archaean Isua metasedimentary rocks". Nature Geoscience. doi:10.1038/ngeo2025. Retrieved 9 Dec 2013. 
  29. ^ Borenstein, Seth (13 November 2013). "Oldest fossil found: Meet your microbial mom". AP News. Retrieved 15 November 2013. 
  30. ^ Noffke, Nora; Christian, Daniel; Wacey, David; Hazen, Robert M. (8 November 2013). "Microbially Induced Sedimentary Structures Recording an Ancient Ecosystem in the ca. 3.48 Billion-Year-Old Dresser Formation, Pilbara, Western Australia". Astrobiology (journal). Bibcode:2013AsBio..13.1103N. doi:10.1089/ast.2013.1030. Retrieved 15 November 2013. 
  31. ^ Schopf J (2006). "Fossil evidence of Archaean life" (PDF). Philosophical Transactions of the Royal Society B 361 (1470): 869–85. doi:10.1098/rstb.2006.1834. PMC 1578735. PMID 16754604. 
  32. ^ Chappe B, Albrecht P, Michaelis W (July 1982). "Polar Lipids of Archaebacteria in Sediments and Petroleums". Science 217 (4554): 65–66. Bibcode:1982Sci...217...65C. doi:10.1126/science.217.4554.65. PMID 17739984. 
  33. ^ Brocks JJ, Logan GA, Buick R, Summons RE (1999). "Archean molecular fossils and the early rise of eukaryotes". Science 285 (5430): 1033–6. doi:10.1126/science.285.5430.1033. PMID 10446042. 
  34. ^ Rasmussen B, Fletcher IR, Brocks JJ, Kilburn MR (October 2008). "Reassessing the first appearance of eukaryotes and cyanobacteria". Nature 455 (7216): 1101–4. Bibcode:2008Natur.455.1101R. doi:10.1038/nature07381. PMID 18948954. 
  35. ^ Hahn, Jürgen; Pat Haug (1986). "Traces of Archaebacteria in ancient sediments". System Applied Microbiology 7 (Archaebacteria '85 Proceedings): 178–83. doi:10.1016/S0723-2020(86)80002-9. 
  36. ^ Wang M, Yafremava LS, Caetano-Anollés D, Mittenthal JE, Caetano-Anollés G (2007). "Reductive evolution of architectural repertoires in proteomes and the birth of the tripartite world". Genome Res. 17 (11): 1572–85. doi:10.1101/gr.6454307. PMC 2045140. PMID 17908824. 
  37. ^ Woese CR, Gupta R (1981). "Are archaebacteria merely derived 'prokaryotes'?". Nature 289 (5793): 95–6. Bibcode:1981Natur.289...95W. doi:10.1038/289095a0. PMID 6161309. 
  38. ^ a b c >Woese C (1998). "The universal ancestor". Proceedings of the National Academy of Sciences of the United States of America 95 (12): 6854–9. Bibcode:1998PNAS...95.6854W. doi:10.1073/pnas.95.12.6854. PMC 22660. PMID 9618502. 
  39. ^ a b Kandler O. The early diversification of life and the origin of the three domains: A proposal. In: Wiegel J, Adams WW, editors. Thermophiles: The keys to molecular evolution and the origin of life? Athens: Taylor and Francis, 1998: 19-31.
  40. ^ Gribaldo S, Brochier-Armanet C (2006). "The origin and evolution of Archaea: a state of the art". Philosophical Transactions of the Royal Society B 361 (1470): 1007–22. doi:10.1098/rstb.2006.1841. PMC 1578729. PMID 16754611. 
  41. ^ a b Woese CR (1 March 1994). "There must be a prokaryote somewhere: microbiology's search for itself". Microbiol. Rev. 58 (1): 1–9. PMC 372949. PMID 8177167. 
  42. ^ Information is from Willey JM, Sherwood LM, Woolverton CJ. Microbiology 7th ed. (2008), Ch. 19 pp. 474–475, except where noted.
  43. ^ Talbert PB, Henikoff S (2010). "Histone variants – ancient wrap artists of the epigenome". Nature Reviews Molecular Cell Biology 11: 264–275. doi:10.1038/nrm2861. 
  44. ^ Sandman K, Reeve JN (2006). "Archaeal histones and the origin of the histone fold". Current Opinion in Microbiology 9: 520–525. doi:10.1016/j.mib.2006.08.003. 
  45. ^ a b c d e Zillig W (1991). "Comparative biochemistry of Archaea and Bacteria". Current Opinion in Genetics & Development 1: 544–551. doi:10.1016/S0959-437X(05)80206-0. 
  46. ^ Bell SD, Jackson SP (April 2001). "Mechanism and regulation of transcription in archaea". Current Opinion in Microbiology 4 (2): 208–13. doi:10.1016/S1369-5274(00)00190-9. PMID 11282478. 
  47. ^ Reeve JN (May 2003). "Archaeal chromatin and transcription". Mol. Microbiol. 48 (3): 587–98. PMID 12694606. 
  48. ^ Kelman LM, Kelman Z (May 2003). "Archaea: an archetype for replication initiation studies?". Mol. Microbiol. 48 (3): 605–15. PMID 12694608. 
  49. ^ Phillips G, Chikwana VM, Maxwell A, et al. (April 2010). "Discovery and characterization of an amidinotransferase involved in the modification of archaeal tRNA". J. Biol. Chem. 285 (17): 12706–13. doi:10.1074/jbc.M110.102236. PMC 2857094. PMID 20129918. 
  50. ^ Koonin EV, Mushegian AR, Galperin MY, Walker DR (1997). "Comparison of archaeal and bacterial genomes: computer analysis of protein sequences predicts novel functions and suggests a chimeric origin for the archaea". Mol Microbiol 25 (4): 619–637. doi:10.1046/j.1365-2958.1997.4821861.x. PMID 9379893. 
  51. ^ a b c d e Gupta R. S. (1998). "Protein phylogenies and signature sequences: A reappraisal of evolutionary relationships among archaebacteria, eubacteria, and eukaryotes". Microbiol. Mol. Biol. Rev 62 (4): 1435–1491. PMC 98952. PMID 9841678. 
  52. ^ Koch AL (2003). "Were Gram-positive rods the first bacteria?". Trends Microbiol 11 (4): 166–170. doi:10.1016/S0966-842X(03)00063-5. PMID 12706994. 
  53. ^ a b c Gupta R.S. (1998). "What are archaebacteria: life's third domain or monoderm prokaryotes related to gram-positive bacteria? A new proposal for the classification of prokaryotic organisms". Mol. Microbiol 29 (3): 695–708. doi:10.1046/j.1365-2958.1998.00978.x. PMID 9723910. 
  54. ^ Brown JR, Masuchi Y, Robb FT, Doolittle WF (1994). "Evolutionary relationships of bacterial and archaeal glutamine synthetase genes". J Mol Evol 38 (6): 566–576. doi:10.1007/BF00175876. PMID 7916055. 
  55. ^ a b c Gupta R.S. (2000). "The natural evolutionary relationships among prokaryotes". Crit. Rev. Microbiol 26 (2): 111–131. doi:10.1080/10408410091154219. PMID 10890353. 
  56. ^ Gupta RS. Molecular Sequences and the Early History of Life. In: Sapp J, editor. Microbial Phylogeny and Evolution: Concepts and Controversies. New York: Oxford University Press, 2005: 160-183.
  57. ^ Cavalier-Smith T (2002). "The neomuran origin of archaebacteria, the negibacterial root of the universal tree and bacterial megaclassification". Int J Syst Evol Microbiol 52 (1): 7–76. PMID 11837318. 
  58. ^ Valas RE, Bourne PE (2011). "The origin of a derived superkingdom: how a Gram-positive bacterium crossed the desert to become an archaeon". Biol Direct 6: 16. doi:10.1186/1745-6150-6-16. PMC 3056875. PMID 21356104. 
  59. ^ Skophammer RG, Herbold CW, Rivera MC, Servin JA, Lake JA (2006). "Evidence that the root of the tree of life is not within the Archaea". Mol Biol Evol 23 (9): 1648–1651. doi:10.1093/molbev/msl046. PMID 16801395. 
  60. ^ Lake JA (January 1988). "Origin of the eukaryotic nucleus determined by rate-invariant analysis of rRNA sequences". Nature 331 (6152): 184–6. Bibcode:1988Natur.331..184L. doi:10.1038/331184a0. PMID 3340165. 
  61. ^ Nelson KE, Clayton RA, Gill SR, et al. (1999). "Evidence for lateral gene transfer between Archaea and bacteria from genome sequence of Thermotoga maritima". Nature 399 (6734): 323–9. Bibcode:1999Natur.399..323N. doi:10.1038/20601. PMID 10360571. 
  62. ^ Gouy M, Li WH (May 1989). "Phylogenetic analysis based on rRNA sequences supports the archaebacterial rather than the eocyte tree". Nature 339 (6220): 145–7. Bibcode:1989Natur.339..145G. doi:10.1038/339145a0. PMID 2497353. 
  63. ^ Yutin N, Makarova KS, Mekhedov SL, Wolf YI, Koonin EV (May 2008). "The deep archaeal roots of eukaryotes". Mol. Biol. Evol. 25 (8): 1619–30. doi:10.1093/molbev/msn108. PMC 2464739. PMID 18463089. 
  64. ^ Lake JA. (1988). "Origin of the eukaryotic nucleus determined by rate-invariant analysis of rRNA sequences". Nature 331 (6152): 184–6. Bibcode:1988Natur.331..184L. doi:10.1038/331184a0. PMID 3340165. 
  65. ^ Williams, Tom A.; Foster, Peter G.; Cox, Cymon J.; Embley, T. Martin (December 2013). "An archaeal origin of eukaryotes supports only two primary domains of life". Nature 504 (7479): 231–236. doi:10.1038/nature12779. PMID 24336283. 
  66. ^ a b c d Krieg, Noel (2005). Bergey's Manual of Systematic Bacteriology. US: Springer. pp. 21–6. ISBN 978-0-387-24143-2. 
  67. ^ Barns, Sue and Burggraf, Siegfried. (1997) Crenarchaeota. Version 1 January 1997. in The Tree of Life Web Project
  68. ^ Walsby, A.E. (1980). "A square bacterium". Nature 283 (5742): 69–71. Bibcode:1980Natur.283...69W. doi:10.1038/283069a0. 
  69. ^ Hara F, Yamashiro K, Nemoto N, et al. (2007). "An actin homolog of the archaeon Thermoplasma acidophilum that retains the ancient characteristics of eukaryotic actin". J. Bacteriol. 189 (5): 2039–45. doi:10.1128/JB.01454-06. PMC 1855749. PMID 17189356. 
  70. ^ Trent JD, Kagawa HK, Yaoi T, Olle E, Zaluzec NJ (1997). "Chaperonin filaments: the archaeal cytoskeleton?". Proceedings of the National Academy of Sciences of the United States of America 94 (10): 5383–8. Bibcode:1997PNAS...94.5383T. doi:10.1073/pnas.94.10.5383. PMC 24687. PMID 9144246. 
  71. ^ Hixon WG, Searcy DG (1993). "Cytoskeleton in the archaebacterium Thermoplasma acidophilum? Viscosity increase in soluble extracts". BioSystems 29 (2–3): 151–60. doi:10.1016/0303-2647(93)90091-P. PMID 8374067. 
  72. ^ a b Golyshina OV, Pivovarova TA, Karavaiko GI, et al. (1 May 2000). "Ferroplasma acidiphilum gen. nov., sp. nov., an acidophilic, autotrophic, ferrous-iron-oxidizing, cell-wall-lacking, mesophilic member of the Ferroplasmaceae fam. nov., comprising a distinct lineage of the Archaea". Int. J. Syst. Evol. Microbiol. 50 (3): 997–1006. doi:10.1099/00207713-50-3-997. PMID 10843038. 
  73. ^ Hall-Stoodley L, Costerton JW, Stoodley P (2004). "Bacterial biofilms: from the natural environment to infectious diseases". Nature Reviews Microbiology 2 (2): 95–108. doi:10.1038/nrmicro821. PMID 15040259. 
  74. ^ Kuwabara T, Minaba M, Iwayama Y, et al. (November 2005). "Thermococcus coalescens sp. nov., a cell-fusing hyperthermophilic archaeon from Suiyo Seamount". Int. J. Syst. Evol. Microbiol. 55 (Pt 6): 2507–14. doi:10.1099/ijs.0.63432-0. PMID 16280518. 
  75. ^ Nickell S, Hegerl R, Baumeister W, Rachel R (2003). "Pyrodictium cannulae enter the periplasmic space but do not enter the cytoplasm, as revealed by cryo-electron tomography". J. Struct. Biol. 141 (1): 34–42. doi:10.1016/S1047-8477(02)00581-6. PMID 12576018. 
  76. ^ Horn C, Paulmann B, Kerlen G, Junker N, Huber H (15 August 1999). "In vivo observation of cell division of anaerobic hyperthermophiles by using a high-intensity dark-field microscope". J. Bacteriol. 181 (16): 5114–8. PMC 94007. PMID 10438790. 
  77. ^ Rudolph C, Wanner G, Huber R (May 2001). "Natural communities of novel archaea and bacteria growing in cold sulfurous springs with a string-of-pearls-like morphology". Appl. Environ. Microbiol. 67 (5): 2336–44. doi:10.1128/AEM.67.5.2336-2344.2001. PMC 92875. PMID 11319120. 
  78. ^ a b Thomas NA, Bardy SL, Jarrell KF (2001). "The archaeal flagellum: a different kind of prokaryotic motility structure". FEMS Microbiol. Rev. 25 (2): 147–74. doi:10.1111/j.1574-6976.2001.tb00575.x. PMID 11250034. 
  79. ^ Rachel R, Wyschkony I, Riehl S, Huber H (March 2002). "The ultrastructure of Ignicoccus: evidence for a novel outer membrane and for intracellular vesicle budding in an archaeon" (PDF). Archaea 1 (1): 9–18. doi:10.1155/2002/307480. PMC 2685547. PMID 15803654. 
  80. ^ a b Koga Y, Morii H (2007). "Biosynthesis of ether-type polar lipids in archaea and evolutionary considerations". Microbiol. Mol. Biol. Rev. 71 (1): 97–120. doi:10.1128/MMBR.00033-06. PMC 1847378. PMID 17347520. 
  81. ^ De Rosa M, Gambacorta A, Gliozzi A (1 March 1986). "Structure, biosynthesis, and physicochemical properties of archaebacterial lipids". Microbiol. Rev. 50 (1): 70–80. PMC 373054. PMID 3083222. 
  82. ^ Albers SV, van de Vossenberg JL, Driessen AJ, Konings WN (September 2000). "Adaptations of the archaeal cell membrane to heat stress". Front. Biosci. 5: D813–20. doi:10.2741/albers. PMID 10966867. 
  83. ^ Damsté JS, Schouten S, Hopmans EC, van Duin AC, Geenevasen JA (October 2002). "Crenarchaeol: the characteristic core glycerol dibiphytanyl glycerol tetraether membrane lipid of cosmopolitan pelagic crenarchaeota". J. Lipid Res. 43 (10): 1641–51. doi:10.1194/jlr.M200148-JLR200. PMID 12364548. 
  84. ^ Koga Y, Morii H (November 2005). "Recent advances in structural research on ether lipids from archaea including comparative and physiological aspects". Biosci. Biotechnol. Biochem. 69 (11): 2019–34. doi:10.1271/bbb.69.2019. PMID 16306681. 
  85. ^ Hanford MJ, Peeples TL (January 2002). "Archaeal tetraether lipids: unique structures and applications". Appl. Biochem. Biotechnol. 97 (1): 45–62. doi:10.1385/ABAB:97:1:45. PMID 11900115. 
  86. ^ Macalady JL, Vestling MM, Baumler D, Boekelheide N, Kaspar CW, Banfield JF (October 2004). "Tetraether-linked membrane monolayers in Ferroplasma spp: a key to survival in acid". Extremophiles 8 (5): 411–9. doi:10.1007/s00792-004-0404-5. PMID 15258835. 
  87. ^ Sára M, Sleytr UB (2000). "S-Layer proteins". J. Bacteriol. 182 (4): 859–68. doi:10.1128/JB.182.4.859-868.2000. PMC 94357. PMID 10648507. 
  88. ^ Engelhardt H, Peters J (1998). "Structural research on surface layers: a focus on stability, surface layer homology domains, and surface layer-cell wall interactions". J Struct Biol 124 (2–3): 276–302. doi:10.1006/jsbi.1998.4070. PMID 10049812. 
  89. ^ a b Kandler, O; König, H (1998). "Cell wall polymers in Archaea (Archaebacteria)" (PDF). Cellular and Molecular Life Sciences (CMLS) 54 (4): 305–308. doi:10.1007/s000180050156. 
  90. ^ Howland, John L. (2000). The Surprising Archaea: Discovering Another Domain of Life. Oxford: Oxford University Press. p. 32. ISBN 0-19-511183-4. 
  91. ^ Gophna U, Ron EZ, Graur D (July 2003). "Bacterial type III secretion systems are ancient and evolved by multiple horizontal-transfer events". Gene 312: 151–63. doi:10.1016/S0378-1119(03)00612-7. PMID 12909351. 
  92. ^ Nguyen L, Paulsen IT, Tchieu J, Hueck CJ, Saier MH (April 2000). "Phylogenetic analyses of the constituents of Type III protein secretion systems". J. Mol. Microbiol. Biotechnol. 2 (2): 125–44. PMID 10939240. 
  93. ^ Ng SY, Chaban B, Jarrell KF (2006). "Archaeal flagella, bacterial flagella and type IV pili: a comparison of genes and posttranslational modifications". J. Mol. Microbiol. Biotechnol. 11 (3–5): 167–91. doi:10.1159/000094053. PMID 16983194. 
  94. ^ Bardy SL, Ng SY, Jarrell KF (February 2003). "Prokaryotic motility structures". Microbiology (Reading, Engl.) 149 (Pt 2): 295–304. doi:10.1099/mic.0.25948-0. PMID 12624192. 
  95. ^ a b c Valentine DL (2007). "Adaptations to energy stress dictate the ecology and evolution of the Archaea". Nature Reviews Microbiology 5 (4): 316–23. doi:10.1038/nrmicro1619. PMID 17334387. 
  96. ^ a b c Schäfer G, Engelhard M, Müller V (1 September 1999). "Bioenergetics of the Archaea". Microbiol. Mol. Biol. Rev. 63 (3): 570–620. PMC 103747. PMID 10477309. 
  97. ^ Romano A, Conway T (1996). "Evolution of carbohydrate metabolic pathways". Res Microbiol 147 (6–7): 448–55. doi:10.1016/0923-2508(96)83998-2. PMID 9084754. 
  98. ^ Koch A (1998). "How did bacteria come to be?". Adv Microb Physiol 40: 353–99. doi:10.1016/S0065-2911(08)60135-6. PMID 9889982. 
  99. ^ DiMarco AA, Bobik TA, Wolfe RS (1990). "Unusual coenzymes of methanogenesis". Annu. Rev. Biochem. 59: 355–94. doi:10.1146/annurev.bi.59.070190.002035. PMID 2115763. 
  100. ^ Klocke M, Nettmann E, Bergmann I, et al. (May 2008). "Characterization of the methanogenic Archaea within two-phase biogas reactor systems operated with plant biomass". Syst. Appl. Microbiol. 31 (3): 190–205. doi:10.1016/j.syapm.2008.02.003. PMID 18501543. 
  101. ^ Based on PDB 1FBB. Data published in Subramaniam S, Henderson R (August 2000). "Molecular mechanism of vectorial proton translocation by bacteriorhodopsin". Nature 406 (6796): 653–7. doi:10.1038/35020614. PMID 10949309. 
  102. ^ Mueller-Cajar O, Badger MR (August 2007). "New roads lead to Rubisco in archaebacteria". BioEssays 29 (8): 722–4. doi:10.1002/bies.20616. PMID 17621634. 
  103. ^ Berg IA, Kockelkorn D, Buckel W, Fuchs G (December 2007). "A 3-hydroxypropionate/4-hydroxybutyrate autotrophic carbon dioxide assimilation pathway in Archaea". Science 318 (5857): 1782–6. Bibcode:2007Sci...318.1782B. doi:10.1126/science.1149976. PMID 18079405. 
  104. ^ Thauer RK (December 2007). "Microbiology. A fifth pathway of carbon fixation". Science 318 (5857): 1732–3. doi:10.1126/science.1152209. PMID 18079388. 
  105. ^ Bryant DA, Frigaard NU (November 2006). "Prokaryotic photosynthesis and phototrophy illuminated". Trends Microbiol. 14 (11): 488–96. doi:10.1016/j.tim.2006.09.001. PMID 16997562. 
  106. ^ Könneke M, Bernhard AE, de la Torre JR, Walker CB, Waterbury JB, Stahl DA (September 2005). "Isolation of an autotrophic ammonia-oxidizing marine archaeon". Nature 437 (7058): 543–6. Bibcode:2005Natur.437..543K. doi:10.1038/nature03911. PMID 16177789. 
  107. ^ Francis CA, Beman JM, Kuypers MM (May 2007). "New processes and players in the nitrogen cycle: the microbial ecology of anaerobic and archaeal ammonia oxidation". ISME J 1 (1): 19–27. doi:10.1038/ismej.2007.8. PMID 18043610. 
  108. ^ Lanyi JK (2004). "Bacteriorhodopsin". Annu. Rev. Physiol. 66: 665–88. doi:10.1146/annurev.physiol.66.032102.150049. PMID 14977418. 
  109. ^ a b Allers T, Mevarech M (2005). "Archaeal genetics — the third way". Nature Reviews Genetics 6 (1): 58–73. doi:10.1038/nrg1504. PMID 15630422. 
  110. ^ Galagan JE, Nusbaum C, Roy A, et al. (April 2002). "The genome of M. acetivorans reveals extensive metabolic and physiological diversity". Genome Res. 12 (4): 532–42. doi:10.1101/gr.223902. PMC 187521. PMID 11932238. 
  111. ^ Waters E, et al. (2003). "The genome of Nanoarchaeum equitans: insights into early archaeal evolution and derived parasitism". Proceedings of the National Academy of Sciences of the United States of America 100 (22): 12984–8. Bibcode:2003PNAS..10012984W. doi:10.1073/pnas.1735403100. PMC 240731. PMID 14566062. 
  112. ^ Schleper C, Holz I, Janekovic D, Murphy J, Zillig W (1 August 1995). "A multicopy plasmid of the extremely thermophilic archaeon Sulfolobus effects its transfer to recipients by mating". J. Bacteriol. 177 (15): 4417–26. PMC 177192. PMID 7635827. 
  113. ^ Sota M; Top EM (2008). "Horizontal Gene Transfer Mediated by Plasmids". Plasmids: Current Research and Future Trends. Caister Academic Press. ISBN 978-1-904455-35-6. 
  114. ^ Xiang X, Chen L, Huang X, Luo Y, She Q, Huang L (2005). "Sulfolobus tengchongensis spindle-shaped virus STSV1: virus-host interactions and genomic features". J. Virol. 79 (14): 8677–86. doi:10.1128/JVI.79.14.8677-8686.2005. PMC 1168784. PMID 15994761. 
  115. ^ Prangishvili D, Forterre P, Garrett RA (2006). "Viruses of the Archaea: a unifying view". Nature Reviews Microbiology 4 (11): 837–48. doi:10.1038/nrmicro1527. PMID 17041631. 
  116. ^ Prangishvili D, Garrett RA (2004). "Exceptionally diverse morphotypes and genomes of crenarchaeal hyperthermophilic viruses". Biochem. Soc. Trans. 32 (Pt 2): 204–8. doi:10.1042/BST0320204. PMID 15046572. 
  117. ^ Pietilä MK, Roine E, Paulin L, Kalkkinen N, Bamford DH (March 2009). "An ssDNA virus infecting archaea; A new lineage of viruses with a membrane envelope". Mol. Microbiol. 72 (2): 307–19. doi:10.1111/j.1365-2958.2009.06642.x. PMID 19298373. 
  118. ^ Mochizuki T, Krupovic M, Pehau-Arnaudet G, Sako Y, Forterre P, Prangishvili D (2012). "Archaeal virus with exceptional virion architecture and the largest single-stranded DNA genome". Proceedings of the National Academy of Sciences of the United States of America 109 (33): 13386–13391. Bibcode:2012PNAS..10913386M. doi:10.1073/pnas.1203668109. PMC 3421227. PMID 22826255. 
  119. ^ Mojica FJ, Díez-Villaseñor C, García-Martínez J, Soria E (2005). "Intervening sequences of regularly spaced prokaryotic repeats derive from foreign genetic elements". J. Mol. Evol. 60 (2): 174–82. doi:10.1007/s00239-004-0046-3. PMID 15791728. 
  120. ^ Makarova KS, Grishin NV, Shabalina SA, Wolf YI, Koonin EV (2006). "A putative RNA-interference-based immune system in prokaryotes: computational analysis of the predicted enzymatic machinery, functional analogies with eukaryotic RNAi, and hypothetical mechanisms of action". Biol. Direct 1: 7. doi:10.1186/1745-6150-1-7. PMC 1462988. PMID 16545108. 
  121. ^ Graham DE, Overbeek R, Olsen GJ, Woese CR (2000). "An archaeal genomic signature". Proceedings of the National Academy of Sciences of the United States of America 97 (7): 3304–8. Bibcode:2000PNAS...97.3304G. doi:10.1073/pnas.050564797. PMC 16234. PMID 10716711. 
  122. ^ a b Gaasterland T (1999). "Archaeal genomics". Current Opinion in Microbiology 2 (5): 542–7. doi:10.1016/S1369-5274(99)00014-4. PMID 10508726. 
  123. ^ Werner F (September 2007). "Structure and function of archaeal RNA polymerases". Mol. Microbiol. 65 (6): 1395–404. doi:10.1111/j.1365-2958.2007.05876.x. PMID 17697097. 
  124. ^ Aravind L, Koonin EV (1999). "DNA-binding proteins and evolution of transcription regulation in the archaea". Nucleic Acids Res. 27 (23): 4658–70. doi:10.1093/nar/27.23.4658. PMC 148756. PMID 10556324. 
  125. ^ Lykke-Andersen J, Aagaard C, Semionenkov M, Garrett RA (September 1997). "Archaeal introns: splicing, intercellular mobility and evolution". Trends Biochem. Sci. 22 (9): 326–31. doi:10.1016/S0968-0004(97)01113-4. PMID 9301331. 
  126. ^ Watanabe Y, Yokobori S, Inaba T, et al. (January 2002). "Introns in protein-coding genes in Archaea". FEBS Lett. 510 (1–2): 27–30. doi:10.1016/S0014-5793(01)03219-7. PMID 11755525. 
  127. ^ Yoshinari S, Itoh T, Hallam SJ, et al. (August 2006). "Archaeal pre-mRNA splicing: a connection to hetero-oligomeric splicing endonuclease". Biochem. Biophys. Res. Commun. 346 (3): 1024–32. doi:10.1016/j.bbrc.2006.06.011. PMID 16781672. 
  128. ^ Rosenshine I, Tchelet R, Mevarech M. (1989) The mechanism of DNA transfer in the mating system of an archaebacterium" Science 245(4924) 1387-1389. PMID 2818746
  129. ^ a b c Fröls S, Ajon M, Wagner M, Teichmann D, Zolghadr B, Folea M, Boekema EJ, Driessen AJ, Schleper C, Albers SV. (2008). UV-inducible cellular aggregation of the hyperthermophilic archaeon Sulfolobus solfataricus is mediated by pili formation" Mol Microbiol 70(4) 938-52. doi: 10.1111/j.1365-2958.2008.06459.x. PMID 18990182
  130. ^ a b c Ajon M, Fröls S, van Wolferen M, Stoecker K, Teichmann D, Driessen AJ, Grogan DW, Albers SV, Schleper C. (2011) UV-inducible DNA exchange in hyperthermophilic archaea mediated by type IV pili" Mol Microbiol 82(4) 807-17. doi: 10.1111/j.1365-2958.2011.07861.x. PMID 21999488
  131. ^ Fröls S, White MF, Schleper C. (2009). Reactions to UV damage in the model archaeon Sulfolobus solfataricus. Biochem Soc Trans 37(1) 36-41. doi: 10.1042/BST0370036. Review. PMID 19143598
  132. ^ Bernstein H and Bernstein C (2013). Evolutionary Origin and Adaptive Function of Meiosis, Meiosis, Dr. Carol Bernstein (Ed.), ISBN 978-953-51-1197-9, InTech, http://www.intechopen.com/books/meiosis/evolutionary-origin-and-adaptive-function-of-meiosis
  133. ^ a b Bernander R (1998). "Archaea and the cell cycle". Mol. Microbiol. 29 (4): 955–61. doi:10.1046/j.1365-2958.1998.00956.x. PMID 9767564. 
  134. ^ Kelman LM, Kelman Z (2004). "Multiple origins of replication in archaea". Trends Microbiol. 12 (9): 399–401. doi:10.1016/j.tim.2004.07.001. PMID 15337158. 
  135. ^ Onyenwoke RU, Brill JA, Farahi K, Wiegel J (2004). "Sporulation genes in members of the low G+C Gram-type-positive phylogenetic branch ( Firmicutes)". Arch. Microbiol. 182 (2–3): 182–92. doi:10.1007/s00203-004-0696-y. PMID 15340788. 
  136. ^ Kostrikina NA, Zvyagintseva IS, Duda VI. (1991). "Cytological peculiarities of some extremely halophilic soil archaeobacteria". Arch. Microbiol. 156 (5): 344–49. doi:10.1007/BF00248708. 
  137. ^ DeLong EF, Pace NR (2001). "Environmental diversity of bacteria and archaea". Syst. Biol. 50 (4): 470–8. doi:10.1080/106351501750435040. PMID 12116647. 
  138. ^ a b Pikuta EV, Hoover RB, Tang J (2007). "Microbial extremophiles at the limits of life". Crit. Rev. Microbiol. 33 (3): 183–209. doi:10.1080/10408410701451948. PMID 17653987. 
  139. ^ Madigan MT, Martino JM (2006). Brock Biology of Microorganisms (11th ed.). Pearson. p. 136. ISBN 0-13-196893-9. 
  140. ^ Takai K, Nakamura K, Toki T, Tsunogai U, Miyazaki M, Miyazaki J, Hirayama H, Nakagawa S, Nunoura T, Horikoshi K (2008). "Cell proliferation at 122°C and isotopically heavy CH4 production by a hyperthermophilic methanogen under high-pressure cultivation". Proceedings of the National Academy of Sciences of the United States of America 105 (31): 10949–54. Bibcode:2008PNAS..10510949T. doi:10.1073/pnas.0712334105. PMC 2490668. PMID 18664583. 
  141. ^ Ciaramella M, Napoli A, Rossi M (February 2005). "Another extreme genome: how to live at pH 0". Trends Microbiol. 13 (2): 49–51. doi:10.1016/j.tim.2004.12.001. PMID 15680761. 
  142. ^ Javaux EJ (2006). "Extreme life on Earth—past, present and possibly beyond". Res. Microbiol. 157 (1): 37–48. doi:10.1016/j.resmic.2005.07.008. PMID 16376523. 
  143. ^ Nealson KH (January 1999). "Post-Viking microbiology: new approaches, new data, new insights". Origins of Life and Evolution of Biospheres 29 (1): 73–93. doi:10.1023/A:1006515817767. PMID 11536899. 
  144. ^ Davies PC (1996). "The transfer of viable microorganisms between planets". Ciba Found. Symp. 202: 304–14; discussion 314–7. PMID 9243022. 
  145. ^ López-García P, López-López A, Moreira D, Rodríguez-Valera F (July 2001). "Diversity of free-living prokaryotes from a deep-sea site at the Antarctic Polar Front". FEMS Microbiol. Ecol. 36 (2–3): 193–202. PMID 11451524. 
  146. ^ Karner MB, DeLong EF, Karl DM (2001). "Archaeal dominance in the mesopelagic zone of the Pacific Ocean". Nature 409 (6819): 507–10. doi:10.1038/35054051. PMID 11206545. 
  147. ^ Giovannoni SJ, Stingl U. (2005). "Molecular diversity and ecology of microbial plankton". Nature 427 (7057): 343–8. Bibcode:2005Natur.437..343G. doi:10.1038/nature04158. PMID 16163344. 
  148. ^ DeLong EF, Karl DM (September 2005). "Genomic perspectives in microbial oceanography". Nature 437 (7057): 336–42. Bibcode:2005Natur.437..336D. doi:10.1038/nature04157. PMID 16163343. 
  149. ^ Konneke M, Bernhard AE, de la Torre JR, Walker CB, Waterbury JB, Stahl DA. (2005). "Isolation of an autotrophic ammonia-oxidizing marine archaeon". Nature 437 (7057): 543–6. Bibcode:2005Natur.437..543K. doi:10.1038/nature03911. PMID 16177789. 
  150. ^ Agogué, H; Brink, M; Dinasquet, J; Herndl, GJ (2008). "Major gradients in putatively nitrifying and non-nitrifying Archaea in the deep North Atlantic". Nature 456 (7223): 788–791. Bibcode:2008Natur.456..788A. doi:10.1038/nature07535. PMID 19037244. 
  151. ^ Teske A, Sørensen KB (January 2008). "Uncultured archaea in deep marine subsurface sediments: have we caught them all?". ISME J 2 (1): 3–18. doi:10.1038/ismej.2007.90. PMID 18180743. 
  152. ^ Lipp JS, Morono Y, Inagaki F, Hinrichs KU (July 2008). "Significant contribution of Archaea to extant biomass in marine subsurface sediments". Nature 454 (7207): 991–4. Bibcode:2008Natur.454..991L. doi:10.1038/nature07174. PMID 18641632. 
  153. ^ Cabello P, Roldán MD, Moreno-Vivián C (November 2004). "Nitrate reduction and the nitrogen cycle in archaea". Microbiology (Reading, Engl.) 150 (Pt 11): 3527–46. doi:10.1099/mic.0.27303-0. PMID 15528644. 
  154. ^ Mehta MP, Baross JA (December 2006). "Nitrogen fixation at 92 degrees C by a hydrothermal vent archaeon". Science 314 (5806): 1783–6. Bibcode:2006Sci...314.1783M. doi:10.1126/science.1134772. PMID 17170307. 
  155. ^ Francis CA, Beman JM, Kuypers MM (May 2007). "New processes and players in the nitrogen cycle: the microbial ecology of anaerobic and archaeal ammonia oxidation". ISME J 1 (1): 19–27. doi:10.1038/ismej.2007.8. PMID 18043610. 
  156. ^ Coolen MJ, Abbas B, van Bleijswijk J, et al. (April 2007). "Putative ammonia-oxidizing Crenarchaeota in suboxic waters of the Black Sea: a basin-wide ecological study using 16S ribosomal and functional genes and membrane lipids". Environ. Microbiol. 9 (4): 1001–16. doi:10.1111/j.1462-2920.2006.01227.x. PMID 17359272. 
  157. ^ Leininger S, Urich T, Schloter M, et al. (August 2006). "Archaea predominate among ammonia-oxidizing prokaryotes in soils". Nature 442 (7104): 806–9. Bibcode:2006Natur.442..806L. doi:10.1038/nature04983. PMID 16915287. 
  158. ^ Baker, B. J; Banfield, J. F (2003). "Microbial communities in acid mine drainage". FEMS Microbiology Ecology 44 (2): 139–152. doi:10.1016/S0168-6496(03)00028-X. PMID 19719632. 
  159. ^ Schimel J (August 2004). "Playing scales in the methane cycle: from microbial ecology to the globe". Proceedings of the National Academy of Sciences of the United States of America 101 (34): 12400–1. Bibcode:2004PNAS..10112400S. doi:10.1073/pnas.0405075101. PMC 515073. PMID 15314221. 
  160. ^ "Trace Gases: Current Observations, Trends, and Budgets". Climate Change 2001. United Nations Environment Programme. 
  161. ^ IPCC AR5 WG1 (2013). "Climate Change 2013: The Physical Science Basis - Summary for Policymakers". Cambridge University Press. 
  162. ^ IPCC AR5 WG1 (2013). "Climate Change 2013: The Physical Science Basis - Anthropogenic and Natural Radiative Forcing Supplementary Material". Cambridge University Press. 
  163. ^ Eckburg P, Lepp P, Relman D (2003). "Archaea and their potential role in human disease". Infect Immun 71 (2): 591–6. doi:10.1128/IAI.71.2.591-596.2003. PMC 145348. PMID 12540534. 
  164. ^ Cavicchioli R, Curmi P, Saunders N, Thomas T (2003). "Pathogenic archaea: do they exist?". BioEssays 25 (11): 1119–28. doi:10.1002/bies.10354. PMID 14579252. 
  165. ^ Lepp P, Brinig M, Ouverney C, Palm K, Armitage G, Relman D (2004). "Methanogenic Archaea and human periodontal disease". Proceedings of the National Academy of Sciences of the United States of America 101 (16): 6176–81. Bibcode:2004PNAS..101.6176L. doi:10.1073/pnas.0308766101. PMC 395942. PMID 15067114. 
  166. ^ Vianna ME, Conrads G, Gomes BP, Horz HP (April 2006). "Identification and quantification of archaea involved in primary endodontic infections". J. Clin. Microbiol. 44 (4): 1274–82. doi:10.1128/JCM.44.4.1274-1282.2006. PMC 1448633. PMID 16597851. 
  167. ^ Waters E, Hohn MJ, Ahel I, et al. (October 2003). "The genome of Nanoarchaeum equitans: insights into early archaeal evolution and derived parasitism". Proceedings of the National Academy of Sciences of the United States of America 100 (22): 12984–8. Bibcode:2003PNAS..10012984W. doi:10.1073/pnas.1735403100. PMC 240731. PMID 14566062. 
  168. ^ Jahn U, Gallenberger M, Paper W, et al. (March 2008). "Nanoarchaeum equitans and Ignicoccus hospitalis: new insights into a unique, intimate association of two archaea". J. Bacteriol. 190 (5): 1743–50. doi:10.1128/JB.01731-07. PMC 2258681. PMID 18165302. 
  169. ^ Baker BJ, Comolli LR, Dick GJ, Hauser LJ, Hyatt D, Dill BD, Land ML, VerBerkmoes NC, Hettich RL, Banfield JF (May 2010). "Enigmatic, ultrasmall, uncultivated Archaeaa". Proceedings of the National Academy of Sciences of the United States of America 107 (19): 8806–8811. Bibcode:2010PNAS..107.8806B. doi:10.1073/pnas.0914470107. PMC 2889320. PMID 20421484. 
  170. ^ Chaban B, Ng SY, Jarrell KF (February 2006). "Archaeal habitats—from the extreme to the ordinary". Can. J. Microbiol. 52 (2): 73–116. doi:10.1139/w05-147. PMID 16541146. 
  171. ^ Schink B (June 1997). "Energetics of syntrophic cooperation in methanogenic degradation". Microbiol. Mol. Biol. Rev. 61 (2): 262–80. PMC 232610. PMID 9184013. 
  172. ^ Lange, M; Westermann, P; Ahring, BK (2005). "Archaea in protozoa and metazoa". Applied Microbiology and Biotechnology 66 (5): 465–474. doi:10.1007/s00253-004-1790-4. PMID 15630514. 
  173. ^ van Hoek AH, van Alen TA, Sprakel VS, et al. (1 February 2000). "Multiple acquisition of methanogenic archaeal symbionts by anaerobic ciliates". Mol. Biol. Evol. 17 (2): 251–8. PMID 10677847. 
  174. ^ Preston, C.M; Wu, K.Y; Molinski, T.F; Delong, E.F (1996). "A psychrophilic crenarchaeon inhabits a marine sponge: Cenarchaeum symbiosum gen. nov., sp. nov". Proceedings of the National Academy of Sciences of the United States of America 93 (13): 6241–6. Bibcode:1996PNAS...93.6241P. doi:10.1073/pnas.93.13.6241. PMC 39006. PMID 8692799. 
  175. ^ Eckburg PB, Bik EM, Bernstein CN, et al. (June 2005). "Diversity of the human intestinal microbial flora". Science 308 (5728): 1635–8. Bibcode:2005Sci...308.1635E. doi:10.1126/science.1110591. PMC 1395357. PMID 15831718. 
  176. ^ Samuel BS, Gordon JI (June 2006). "A humanized gnotobiotic mouse model of host-archaeal-bacterial mutualism". Proceedings of the National Academy of Sciences of the United States of America 103 (26): 10011–6. Bibcode:2006PNAS..10310011S. doi:10.1073/pnas.0602187103. PMC 1479766. PMID 16782812. 
  177. ^ Wegley, L; Yu, Y; Breitbart, M; Casas, V; Kline, D.I; Rohwer, F (2004). "Coral-associated Archaea" (PDF). Marine Ecology Progress Series 273: 89–96. doi:10.3354/meps273089. 
  178. ^ Chelius MK, Triplett EW (April 2001). "The Diversity of Archaea and Bacteria in Association with the Roots of Zea mays L". Microb. Ecol. 41 (3): 252–63. doi:10.1007/s002480000087. PMID 11391463. 
  179. ^ Simon HM, Dodsworth JA, Goodman RM (October 2000). "Crenarchaeota colonize terrestrial plant roots". Environ. Microbiol. 2 (5): 495–505. doi:10.1046/j.1462-2920.2000.00131.x. PMID 11233158. 
  180. ^ Breithaupt H (2001). "The hunt for living gold. The search for organisms in extreme environments yields useful enzymes for industry". EMBO Rep. 2 (11): 968–71. doi:10.1093/embo-reports/kve238. PMC 1084137. PMID 11713183. 
  181. ^ a b Egorova K, Antranikian G (2005). "Industrial relevance of thermophilic Archaea". Current Opinion in Microbiology 8 (6): 649–55. doi:10.1016/j.mib.2005.10.015. PMID 16257257. 
  182. ^ Synowiecki J, Grzybowska B, Zdziebło A (2006). "Sources, properties and suitability of new thermostable enzymes in food processing". Crit Rev Food Sci Nutr 46 (3): 197–205. doi:10.1080/10408690590957296. PMID 16527752. 
  183. ^ Jenney FE, Adams MW (January 2008). "The impact of extremophiles on structural genomics (and vice versa)". Extremophiles 12 (1): 39–50. doi:10.1007/s00792-007-0087-9. PMID 17563834. 
  184. ^ Schiraldi C, Giuliano M, De Rosa M (2002). "Perspectives on biotechnological applications of archaea" (PDF). Archaea 1 (2): 75–86. doi:10.1155/2002/436561. PMC 2685559. PMID 15803645. 
  185. ^ Norris PR, Burton NP, Foulis NA (2000). "Acidophiles in bioreactor mineral processing". Extremophiles 4 (2): 71–6. doi:10.1007/s007920050139. PMID 10805560. 
  186. ^ Shand RF; Leyva KJ (2008). "Archaeal Antimicrobials: An Undiscovered Country". In Blum P (ed.). Archaea: New Models for Prokaryotic Biology. Caister Academic Press. ISBN 978-1-904455-27-1. 

Further reading

  • Howland, John L. (2000). The Surprising Archaea: Discovering Another Domain of Life. Oxford: Oxford University Press. ISBN 0-19-511183-4. 
  • Martinko JM, Madigan MT (2005). Brock Biology of Microorganisms (11th ed.). Englewood Cliffs, N.J: Prentice Hall. ISBN 0-13-144329-1. 
  • Garrett RA, Klenk H (2005). Archaea: Evolution, Physiology and Molecular Biology. WileyBlackwell. ISBN 1-4051-4404-1. 
  • Cavicchioli R (2007). Archaea: Molecular and Cellular Biology. American Society for Microbiology. ISBN 1-55581-391-7. 
  • Blum P (editor) (2008). Archaea: New Models for Prokaryotic Biology. Caister Academic Press. ISBN 978-1-904455-27-1. 
  • Lipps G (2008). "Archaeal Plasmids". Plasmids: Current Research and Future Trends. Caister Academic Press. ISBN 978-1-904455-35-6. 
  • Sapp, Jan (2009). The New Foundations of Evolution. On the Tree of Life. New York: Oxford University Press. ISBN 0-19-538850-X. 
  • Schaechter, M (2009). Archaea (Overview) in The Desk Encyclopedia of Microbiology, 2nd edition. San Diego and London: Elsevier Academic Press. ISBN 978-0-12-374980-2. 

External links

General

Classification

Genomics