environmental, biogeographic, and biochemical …aem.asm.org/content/77/15/5071.full.pdfing their...

APPLIED AND ENVIRONMENTAL MICROBIOLOGY, Aug. 2011, p. 5071–5078 Vol. 77, No. 150099-2240/11/$12.00 doi:10.1128/AEM.00726-11Copyright © 2011, American Society for Microbiology. All Rights Reserved.

Environmental, Biogeographic, and Biochemical Patterns ofArchaea of the Family Ferroplasmaceae�

Olga V. Golyshina*School of Biological Sciences, Bangor University, LL57 2UW Gwynedd, Wales, United Kingdom

About 10 years ago, a new family of cell wall-deficient, iron-oxidizing archaea, Ferroplasmaceae, within thelarge archaeal phylum Euryarchaeota, was described. In this minireview, I summarize the research progressachieved since then and report on the current status of taxonomy, biogeography, physiological diversity,biochemistry, and other research areas involving this exciting group of acidophilic archaea.

Microorganisms thrive remarkably under various conditions,including high temperatures, extremely high osmosis, and veryacidic pH, that would generally be considered hostile or lim-iting to higher organisms. Studying and understanding theuniqueness of extremophilic organisms and the biochemicaland cellular processes underlying their functioning and role inbiogeochemical processes comprise an emerging research areain modern bioscience. Of special interest for various biotech-nological applications are enzymes produced by extremophiles,the so-called extremozymes, which exhibit a high activity andstability under extreme physical-chemical conditions. The rep-resentatives of the “third domain of life,” the archaea, areunique contributors to this area of special interest. Severalfactors make the archaea an attractive subject of study, includ-ing their relatively recent history of discovery, ability (oftenmuch higher than that of bacteria) to adapt to harsh environ-ments, enigmatic nature, and low cultivability.

This minireview focuses on acidophiles representing theeuryarchaeal family Ferroplasmaceae, first described about a de-cade ago (25), and on some aspects relevant to their physiology,geographic distribution, and taxonomic diversity. Representativesof this family are cell wall-lacking extreme and obligate acido-philes that are able to grow at pH values around 0. Together withtheir closest phylogenetic neighbors, from the family Picrophi-laceae, they comprise a group of the most extreme acidophilicorganisms known. Furthermore, the Ferroplasmaceae thrive insystems with high concentrations of iron, copper, zinc, and othermetals. Archaea of the family Ferroplasmaceae coexist in theirnatural habitats with other acidophilic or acid-tolerant pro-karyotes, namely, members of the bacterial phyla Firmucutes,Proteobacteria, Actinobacteria, and Nitrospirae, representatives ofthe Crenarchaeota, and other Euryarchaeota that are importantdrivers in environmental acid generation and in global cycling ofiron and sulfur. Accordingly, being important iron oxidizers, theorganisms of the family Ferroplasmaceae significantly contributeto these processes.

Biogeography. The members of the family Ferroplasmaceaeare distributed worldwide (Fig. 1) and can be found in a varietyof acidic environments with very stable chemical conditions,such as ore deposits, mines, and acid mine drainage systems

(natural or man-made), and in areas with geothermal activity.Detection or quantification of the Ferroplasmaceae in theseenvironments was done mostly using small subunit (SSU)rRNA-targeting analyses, such as 16S rRNA gene clone librar-ies’ sequencing, amplified rRNA gene restriction analysis(ARDRA) profiling, real-time quantitative PCR, restrictionfragment length polymorphism (RFLP) or fluorescence in situhybridization (FISH), and oligonucleotide microarray analysis,all of which revealed the presence of these archaea in a num-ber of pyritic/arsenopyritic, gold-arsenopyritic/chalcopyritic,and lead-, zinc-, and copper-containing mines across all conti-nents (11, 24, 26, 45, 46, 51, 55, 56, 57, 58). Clones related tothe family Ferroplasmaceae have also been documented in fur-ther natural sulfide-rich ecosystems, e.g., in the snottites, i.e.,the stalactite-like formations of microbial origin taken fromthe walls of Frasassi Cave and in the Rio Garrafo cave systems,both located in Italy, where acidic microenvironments wereformed as a result of sulfide oxidation (38). Acid mine drainagesystems of Richmond Mine on Iron Mountain (California) andRio-Tinto (Spain) have been extensively studied as environ-ments hosting the Ferroplasmaceae (1, 3, 18, 23, 29). For yearsthe family Ferroplasmaceae was represented by a single mono-specific genus, Ferroplasma, containing only a single specieswith a validly published name, Ferroplasma acidiphilum YT

DSM 12658T (25). Further isolates belonging to the genusFerroplasma have been obtained, such as “Ferroplasma acidar-manus” fer1 (18) and a few others, with SSU rRNA identical tothat of F. acidiphilum or just with few mismatches (12, 16, 40,41; D. B. Johnson, personal communication) (Fig. 2). A newgenus, Acidiplasma, of the family Ferroplasmaceae has veryrecently been described as containing two species, named Aci-diplasma aeolicum VT (DSM 18409T � JCM 14615T) and A.cupricumulans (DSM 16551T � JCM 13668T), isolated fromthe hydrothermal pool located on Vulcano Island (Italy) andfrom chalcocite/copper-containing heaps (Myanmar), respec-tively (28, 30, 31). A few other Acidiplasma-like strains havebeen isolated from pyrite- and chalcopyrite-leaching bioreac-tors (59). It should also be noted that A. aeolicum is not theonly representative of the family Ferroplasmaceae isolatedfrom sites with high geothermal activity, rich in ferrous sul-fides, hydrogen sulfides, and sulfur dioxide. There are quite anumber of similar moderately thermophilic strains isolated byour laboratory from South Europe’s stratovolcanos, with highhydrothermal activity observed on the sites in forms of hotsprings along the costs, solfataras, and fumaroles (Fig. 3).

* Mailing address: School of Biological Sciences, Bangor University,LL57 2UW Gwynedd, Wales, United Kingdom. Phone: 44 1248383629. Fax: 44 1248 38 25 69. E-mail: [email protected].

� Published ahead of print on 17 June 2011.

5071

on June 15, 2018 by guesthttp://aem

.asm.org/

Dow

nloaded from

http://aem.asm.org/

Sequences of archaea of the family Ferroplasmaceae werealso recovered from Red Sea samples taken from Atlantis II,the world’s largest marine polymetallic ore body (R. Z. Abdal-lah, personal communication). Many questions arise in con-nection with these local environmental conditions, such as at-mosphere, salinity, pH range, and general features of seawaterpromoting buffering capacity. However, the findings summa-rized above undoubtedly represent only a very small propor-tion of still-undetected and uncharacterized family members.

In seeking an explanation for why the Ferroplasmaceae areso globally ubiquitous (which is reflected in numerous litera-ture references and sequence databases’ entries), one mightconsider the global abundance of iron, which is the fourth mostabundant chemical element in the Earth’s crust and is found inconcentrated deposits widely distributed across all continents.The iron-containing mineral pyrite is the most ubiquitous sul-fide mineral on Earth, accumulated in sites of hydrothermalorigin and found in igneous, sedimentary, and metamorphic

FIG. 1. The geographic distribution of members of the family Ferroplasmaceae: the isolates (red squares) and 16S rRNA gene signatures (blacksquares).

FIG. 2. The neighbor-joining phylogenetic tree constructed on the basis of 16S rRNA gene sequences of isolates of the order Thermoplasma-tales. Two very distinct clusters in the family Ferroplasmaceae can be seen to represent two genera, Ferroplasma and Acidiplasma.

5072 MINIREVIEWS APPL. ENVIRON. MICROBIOL.


.asm.org/

Dow

nloaded from

http://aem.asm.org/

rocks. It is quite obvious that different acidic ecosystems withextremely low or moderate-value pHs and high concentrationsof iron favorable to iron-oxidizing acidophiles exist in manylocations on our Planet. It may also be suggested that there isa sampling bias that favors acid mine drainage (AMD) systems

or ore deposits because of biotechnological/commercial impor-tance and their contribution to environmental pollution. In-deed, AMD streams are the cause of a significant negativeimpact on the surrounding ecosystems due to their contribu-tion of highly acidic waters containing high concentrations of

FIG. 3. Examples of sites of recent isolation or enrichments of Ferroplasmaceae. The sample sites are marked with white arrows. (A) Rockoutcrops/sample at the old copper mine Parys Mountain (Anglesey, United Kingdom). The enrichment in the medium 9K contains an organismclosely related to F. acidiphilum (O. V. Golyshina, unpublished). (B) The hydrothermal pool on Vulcano Island (Italy), the origin of the isolationof Acidiplasma aeolicum VT. The culture was initially enriched from the sand/gravel-containing material (right panel) (28). (C) The outlet (rightpanel) of the hot spring (left panel) on Sao Miguel Island (Azores, Portugal). The 16S rRNA clone library from the enrichment established withthe surface sulfur-containing sample contained sequences closely related to Acidiplasma aeolicum (Golyshina, unpublished).

VOL. 77, 2011 MINIREVIEWS 5073


.asm.org/

Dow

nloaded from

http://aem.asm.org/

toxic soluble metals to the rivers, seas, and oceans. Further,volcanic acidic environments associated with tectonic activitiesare another sampling “hot spot” and attract the increasingattention of microbiologists who seek unusual microorganismsand an understanding of their biogeochemical activities. Vul-cano Island is an example of an extensively sampled yet unex-hausted geothermally active site, where a few dozen new spe-cies of thermophilic archaea and bacteria have already beenisolated and described. On the other hand, a feasible explana-tion for the occurrence of the Ferroplasmaceae in such envi-ronments, with conditions that are relatively consistent interms of pH and high concentrations of soluble iron, are theirrelatively small genomes, predetermining metabolism and nar-rowing their niche, as discussed earlier (26). The Ferroplas-maceae exhibit a combination of physiological traits comparedto other acidophilic prokaryotes that will further be discussedin detail below (see “Physiological variability within Ferroplas-maceae”).

It is interesting to mention that the strains VT (A. aeolicum)and BH2T (A. cupricumulans), isolated from geographicallydistinct regions and from geologically and geochemically dis-tinct ecosystems (Vulcano Island [Italy] and a mine in Myan-mar; acidic volcanic pool and chalcocite- and copper-contain-ing ore, correspondingly) exhibit no mismatches in their 16SrRNA gene sequence; however, the results of DNA-DNA hy-bridization revealed that the strains indeed belong to two dif-ferent species (28).

The same is also true for many members of the Ferroplas-maceae isolated from various locations (Fig. 3): most membersof Ferroplasma spp. (16) and Acidiplasma spp. exhibited iden-tical 16S rRNA gene sequences within corresponding genera.This does not necessarily mean that all strains belong to thesame species and are not distinct physiologically, since thenatural variability of mineral substrates, pH, different types ofores, etc., in isolation sites represents a very powerful naturalforce for evolution and speciation.

In the past few years, numerous examples of unculturedThermoplasmatales, the so-called “alphabet plasmas,” detectedin clone libraries or found in metagenomic sequencing datasets derived from a great variety of environments, haveemerged (for a few, see references 3, 38, and 45). SSU rRNAgene sequences of “alphabet plasmas” have a very broad phy-logenetic diversity across the order Thermoplasmatales. It is notclear if the epithet “plasma” is appropriate in the context ofcellular morphology, i.e., whether these organisms lack the cellwall, since even within Thermoplasmatales, the archaea fromgenus Picrophilus spp. have a rigid cellular envelope (49, 50)and thus cannot be considered “-plasmas.” I therefore believe,to avoid further confusion, these organisms must be defined as“members of Thermoplasmata/Thermoplasmatales” or anothertaxon, depending on their affiliation within a commonly recog-nized taxonomic boundary.

Physiological variability within Ferroplasmaceae. All mem-bers of the family Ferroplasmaceae, with minor exceptions,share quite similar physiological traits, which to some extentmakes it difficult to distinguish isolates for provision of taxo-nomic descriptions. According to the opinion of Valentine(53), the physiology and phylogeny are generally more cohe-sive in archaea than in bacteria. For example, Valentine placesthe physiologically coherent halophilic archaea that form a

phylogenetically tightly clustering group of 22 genera withinjust one class, known as Halobacteria, which is in sharp contrastto phylogenetically diverse halophilic bacteria that span morethan 10 different classes of Bacteria. All members of the familyFerroplasmaceae that have been physiologically characterizedshare extreme acidophily (optimal pH range of 0.8 to 1.8), aubiquitous capacity for ferrous iron oxidation (within this fam-ily, there are no isolates known that are unable to oxidizeferrous iron), and a strict dependence on a low concentrationof yeast extract, common for a vast majority of archaea. Somevariations among strains of the two genera comprising theFerroplasmaceae are known in relation to the ability for che-moorganotrophy, aerobic or facultative anaerobic growth, ortemperature growth optima (mesophilic or moderately ther-mophilic). Mesophilic or moderate thermophilic Ferroplas-maceae exhibit growth at optimal temperatures from 35°C forthe most mesophilic strains to 55°C for the majority of ther-mophilic isolates. Being able to outperform the competitors atmoderate temperatures or across a relatively wide temperaturerange is an important option for these iron oxidizers sinceiron/pyrite oxidation is an exothermic process. CO2 fixationrates in F. acidiphilum strains YT and Y-2 were reported to berelatively low, approximately 12 times lower than those in theoptimally grown, iron-oxidizing bacterium Acidithiobacillus fer-rooxidans (41), a margin similar to that observed for growthrates which are generally low in all members of the Ferroplas-maceae (16, 25). However, Acidiplasma aeolicum VT grownchemoorganotrophically on glucose and yeast extract, whileexhibiting lower growth rates, produces higher biomass yieldsper unit of consumed substrate (28). Karavaiko and coauthors(34) suggested that the occurrence of more-diverse variants ofmetabolism, e.g., mixotrophy and general reduction of auto-trophy in environments with higher temperatures, is a functionof the lower solubility of both oxygen and CO2 required foriron oxidation and autotrophy. Heterotrophic metabolism insome members of the Ferroplasmaceae may function as anecological advantage, enabling this group to operate as doThermoplasma spp., by scavenging organic matter produced inmicrobial biofilms that are typically formed in iron-based nat-ural environments.

Most of the strains of the Ferroplasmaceae (a majority of F.acidiphilum strains, A. cupricumulans BH2, A. aeolicum V, andfurther strains of A. aeolicum [O. V. Golyshina, unpublished])have been found and isolated from solid ores and minerals,volcanic soils, ash particles, or sand/gravel samples or frombiofilms and microbial mats (e.g., “F. acidarmanus” fer1 [18]),indicating that the solid-phase-attached, rather than plank-tonic, cell forms are prevalent in nature. In this relation, thehigh level of adhesion of F. acidiphilum YT cells to the surfaceof pyrite under acidic conditions was studied and explainedthrough the prism of the Deryagin-Landau-Verwey-Overbeek(DLVO) theory, i.e., considering the interaction of twocharged surfaces via a thin liquid layer (19). Two differenttypes of biofilm morphology have been found to be producedby the strain “F. acidarmanus” fer1, and further prevalence ofthe anaerobic type of metabolism has been observed in maturebiofilms (7). However, no common quorum-sensing signalingmolecules have been detected by the authors in the aqueousphase of bioreactors. Given that the Ferroplasmaceae are non-motile, they may not necessarily require an extra chemical



.asm.org/

Dow

nloaded from

http://aem.asm.org/

signal to adhere. Additional studies will be of a great impor-tance for further understanding the mechanisms and kineticsof cellular attachment of the Ferroplasmaceae to solid surfaces.

Lipid biomarkers. Archaeal tetraether-based lipids are con-sidered to play a pivotal role in maintaining the pH gradientacross the cellular membrane (36, 54). The chemical compo-sition of membrane lipids is therefore a relevant, if not the onlyuseful, marker for chemotaxonomy in those archaea. Majormembrane lipids of the family members are dibiphytanyl-basedtetraether lipids. The polar lipids were reported to be mostlysingle phosphoglycolipid derivatives based on a galactosyl dibi-phytanyl phosphoglycerol tetraether, with minor amounts ofmono- and diglycosyl dibiphytanyl ether lipids; and the mainrespiratory quinones were found to be naphthoquinone deriv-atives (8, 28). F. acidiphilum YT and Y-2 have been reported tohave a �-D-glucose moiety in their major glycosyl dibiphytanylphosphoglycerol lipid (8), whereas the sugar residue in A.aeolicum VT was reported to be �-galactopyranose (28). Un-doubtedly, it is hard to overstate the role of chemotaxonomy inprovision of an unambiguous identity of new isolates for theiraffiliation at the genus level within Ferroplasmaceae and withinhierarchically higher taxonomic divisions, especially as a resultof poor resolution of SSU rRNA within a single genus.

Viral control in acidophilic microbial communities. Micro-bial life in acidic ecosystems is controlled by factors similar tothose in any other microbial community: competitive interac-tions, predation, and syntrophic and mutualistic interactions,to name a few (32). Viruses seem to play an important role inenvironments populated by the Ferroplasmaceae. In someacidic systems, e.g., geothermally active sites, environmentswith temperatures above 80°C have been known to have lowernumbers of viruses than other ecosystems due to challenginglylow pH and high temperatures. Nonetheless, even under suchextreme conditions, viruses can effectively control microbialdensities, significantly influencing biogeochemical cycles andacting as drivers of microbial evolution (43, 47). At least twoviral morphotypes and virus-host associations have been ob-served in a cryo-electron microscopy study of ultrasmall ar-chaeal “ARMAN” cells from biofilm samples from the Rich-mond Mine at Iron Mountain (California) (13). A furtherconfirmation of the presence of viruses in the environmentspopulated inter alia by members of the Ferroplasmaceae isreferred to in documentations about the presence of sequencesof CRISPR, CRISPR-associated cas genes, and prophage-as-sociated genes identified in the process of metagenomic datamining from samples from Richmond Mine (Iron Mountain)by the group led by J. F. Banfield. CRISPR-containing lociwere initially identified in large metagenome assemblies toharbor approximately 2,400 unique spacer regions, which werefurther compared to all contigs and unassembled reads. Afterthat, the spacer-based reconstruction of genome fragments ofviruses was performed, and finally, the pairing matches be-tween hosts and viruses were established. The observed prev-alent matching of only very recently acquired spacers to cor-responding viruses suggested a high rate of resistanceemergency in acid mine drainage systems (2, 15). About 24putative prophage-associated genes have been identified in thegenome of the strain “F. acidarmanus” fer1; prophage-associ-ated genes were also present in the 8-Mbp metagenomic se-quencing data set obtained by shotgun sequencing of small-

insert libraries derived from the DNA sample from RichmondMine; importantly, from the isolation site of the strain“F. acidarmanus” fer1 (1). Analysis showed that the gene in-sertion and loss of genes, possibly of phage origin, and thepresence of numerous transposases are important factors forincreasing heterogeneity within the local population (1).

Iron-containing proteins in Ferroplasma. Since organismsfrom the family Ferroplasmaceae exhibit a number of unusualphysiological traits, one can assume that the biochemistry un-derlying their ability to exist at the known limits of life is alsorather unusual. Indeed, a number of studies have been under-taken to gain a deeper insight into the structural-functionalpeculiarities of proteins from cultured representatives of theFerroplasmaceae. Investigations on helicase Rad3 from “F. aci-darmanus” showed the importance of the FeS cluster for “thefolding and stability of the auxiliary domain uniquely charac-teristic to the Rad3 helicase” (44). A number of remarkablecharacteristics have also been discovered in proteins from F.acidiphilum YT. Interestingly, a few cloned and heterologouslyexpressed (in E. coli) intracellular or membrane-associatedenzymes, namely, three alpha-glycosidases, esterase, andDNA-ligase, exhibited very low pH optima in vitro, or “pHoptimum anomaly” (26, 27). Cloned enzymes were most activein the pH range 1.7 to 4.0, which is unusually low. A possibleexplanation was that the low pH in vitro is mimicking positivecharges of amino acids and cations accumulating in the cyto-plasm to electrostatically compensate the high proton gradientacross the membrane via establishing a high positive mem-brane potential (��) (inside positive), which is the knownmechanism for adaptation to the acidity described for eukary-otic cellular structures such as positively charged secretoryvacuoles, lysosomes, and mitochondria, where an acidic pH isnecessary for certain activities. An alternative but rather spec-ulative explanation was a possible cytoplasmic heterogeneity orcellular compartmentalization (27). Among proteins from Fer-roplasma spp. characterized thus far, perhaps the most strikingwas the DNA ligase from F. acidiphilum YT (LigFa), the evo-lutionarily very conserved enzyme important for maintenanceof the integrity of DNA in the cell, especially in the context ofdamaging effects of acid and oxidative stress caused by reactiveforms of iron. Comparative characterization of DNA ligasesfrom F. acidiphilum and from other hyperacidophilic archaeaand phylogenetic neighbors, namely, from Thermoplasma aci-dophilum and Picrophilus torridus, from Sulfolobus acidocal-darius (Crenarchaeota, inhabiting acidic, metal- and sulfur-richhigh-temperature ecosystems), and from an acidophilic iron-oxidizing bacterium, Acidithiobacillus ferrooxidans, revealedthe uniqueness of the purple-colored LigFa enzyme with re-spect to its extremely low pH optimum in vitro and unusualferric iron dependency, which contrasts with the magnesium orpotassium requirement common in DNA ligases (21). TheLigFa is phylogenetically related to DNA ligases from othermembers of the Thermoplasmatales (T. acidophilum and P.torridus), and as it turned out, all of them depend on both ATPand NAD�, whereas ligases from S. acidocaldarius and A.ferrooxidans were exclusively ATP dependent. The dual cofac-tor dependence has also been described for members of othereuryarchaeotic orders, Thermococcales, Thermococcus kodak-araensis, and Thermococcus fumicolans, archaea phylogeneti-cally very close to Thermoplasmatales and functioning at high



.asm.org/

Dow

nloaded from

http://aem.asm.org/

or very high temperatures (39, 48). The LigFa together withother ligases from archaea of the order Thermoplasmatales is,rather, phylogenetically placed within a cluster of ligases fromCrenarcheota, which is indeed an indication of a special andsomewhat unclear placement of Thermoplasmatales on theoverall archaeal map. Coincidently, some proteins present inalmost all members of the Euryarchaeota were reported to bemissing in the Thermoplasmatales, and conversely, there is acertain core of proteins encoded in the genomes of the Ther-moplasmatales which allows one to speculate about a deeperbranching of this order within the phylum Euryarchaeota (22).Sequence analysis revealed about 77 archaeon-specific pro-teins uniquely present only in Thermoplasmata, of which 17unique proteins were shared by P. torridus and “F. acidarma-nus”; almost all of those were annotated as hypothetical pro-teins. Gao and Gupta (22) have indicated that the members ofthe order Thermoplasmatales are the closest euryarchaea to thebranching point where the Euryarchaeota and Crenarchaeotaemerged, a concept supported by data on distribution of spe-cific archaeal proteins encoded by representative genomes.

Apart from individually cloned and characterized enzymes,iron-containing proteins have further been identified in thetotal proteome of F. acidiphilum YT (20). About 85% of allproteins in the analyzed proteome retained iron in stoichio-metric amounts, and as revealed by the experimental analysisof a subset of proteins picked at random, this element wasessential for protein structure and for function. Among theanalyzed items were many housekeeping proteins never re-ported to contain iron or other metals. Importantly, the ob-served ubiquity of iron-containing proteins was not observed inphylogenetically or physiologically related microorganisms, ei-ther in other members of the Thermoplasmatales or in iron-grown A. ferrooxidans: it was an exclusive attribute of F. acid-iphilum YT. Based on this observation, a hypothesis wasproposed that iron became a major structure-determiningcomponent in Ferroplasma proteins, since these organisms per-manently thrived in (and never escaped from) the iron-richenvironments that were dominant under primordial conditionson Earth but have become extinct since then. In other micro-organisms that further evolved outside iron-rich niches, thestructural function of iron had to be substituted for by otherelements or mechanisms due to the low availability of theformer. According to this hypothesis, Ferroplasma represents arelic form of life with a very special evolutionary trajectory.

Copper and arsenic resistance. The Ferroplasmaceae oftenfunction at high concentrations of iron, and depending on themineral composition of ores or rocks, copper and arsenic mayalso be present in quantities toxic for most prokaryotes. Obvi-ously, adaptation mechanisms are essential for archaea oper-ating under such conditions, especially in bioleaching systems.Studies of resistance mechanisms have been carried out withcultures of “F. acidarmanus” fer1 (5, 6). Using proteome anal-ysis, multiple pathways of resistance have been recorded to beactivated at copper concentrations of up to 20 g Cu2� liter�1:the induction of DNA repair proteins, such as RadA, type II60-kDa chaperonins, and chaperone DnaK homologs. Tran-scription analysis revealed an increase in two mRNA species,transcribed from the genes copZ, encoding the metal bindingprotein, and copB, encoding the copper-transporting P-typeATPase, in response to high levels of copper (5). Arsenic

resistance of the strain “F. acidarmanus” fer1 against up to a133 mM concentration of arsenite was suggested to be deter-mined by a known As(III) reduction mechanism, whereas nogenes for arsenate reductase have been found in the draftgenome of “F. acidarmanus” fer1 and the pathway to cope withAs(V) was proposed to be entirely novel (6).

Methanethiol production. The microbial production ofmethanethiol is important from an ecological point of view asa contribution to sulfur cycling and considering its potentialrole as a greenhouse gas; the degradation of methanethiol insome environments, such as freshwater sediments, has alsobeen proposed to be linked to methanogenic activity (37). Anobservation about methanethiol production by “F. acidarma-nus” has been presented (10). Radiolabeled methionine, cys-teine, and sulfate were used for methanethiol production byheterotrophically or chemolithotrophically grown “F. acidar-manus”. This study, together with another survey of a hightypical sulfate concentration for growth of this archaeon, con-tributes to the understanding of the role of these archaea in thesulfur cycle in the biosphere (9). The ecological role of meth-anethiol production by “F. acidarmanus” was proposed to be asa substrate or chemotactic signal for the other communitymembers (10). That compound seems to be an additional(physiological) link between phylogenetically/evolutionarily re-lated methanogenes and members of the order Thermoplasma-tales, where the family Ferroplasmaceae is accommodated aswell.

Genomics of Ferroplasmaceae. Members of the Ferroplas-maceae are widely represented in acidic environments thatwere recently subjected to extensive environmental genomicsstudies (4, 52). Later, the genome sequencing of the isolate“F. aciadarmanus” fer1 was conducted (1). The genome se-quence assembly of “F. acidarmanus” fer1 was obtained from41,779 small-insert library reads and additional 1,537 end se-quences delivered from a fosmid library. The resulting draftgenome contained a number of gaps, which have been filledusing the metagenome data. The size of the genome was re-ported to be 1.94 Mb, with 1,963 predicted open readingframes (ORFs), of which 69.4% were genes with functionalpredictions and 15.3% and 15.2% were represented by con-served hypothetical and hypothetical proteins. The study wasaccompanied by comparative genome analysis of the fer1 iso-late with its environmental population, fer1(env), from thesame sampling site. Given the high abundance of the Ferro-plasmaceae in the sample, the total of 103 Mb of combinedenvironmental sequencing data from different samples coveredalmost 92% of the fer1 genome. The difference between fer1and fer1(env) genomes was in just 45 genes present in theenvironmental population but missing in the fer1 isolate and152 genes occurring in the isolate and not present in the com-posite fer1(env) data. Corresponding gene products weremostly conserved hypothetical and hypothetical proteins, in-tegrases, transposases, restriction/modification, DNA re-pair, and transport proteins, and glycosyltransferases. Further-more, there were clear indications of genomic heterogeneitywithin the natural population, with a predominance of a smallnumber of sequence types and a strong stabilizing selection foralmost all genes (1). Apparent genome rearrangements in theisolate fer1 detected after comparison of Sanger sequencingdata sets from a small-insert library and fosmids established a



.asm.org/

Dow

nloaded from

http://aem.asm.org/

few years after the latter were the likely cause of gaps in thegenome assembly. Such genome instability was reported ear-lier for Ferroplasma acidiphilum isolates (35). The availabilityof genomic data for Ferroplasma spp. has stimulated a numberof studies for experimental validation of physiological implica-tions of genome-based in silico metabolic reconstructions con-ducted in earlier investigations pioneered by Tyson and col-leagues (52). In particular, blue copper-heme sulfocyanin andcytochrome cbb3 have been suggested to play an important rolein ferrous oxidation and to act as a terminal electron acceptor,respectively (17). A very recent proteome study has pinpointeda number of proteins involved in iron homeostasis in the Fer-roplasmaceae (42).

Concluding remarks. The wide geographical disseminationacross all continents, their ecological importance in iron andsulfur cycling, and the uniqueness of their biochemical machin-ery make the microorganisms comprising the family Ferroplas-maceae an important subject for studies in general microbiol-ogy, biochemistry, microbial evolution, origins of life,astrobiology, and biotechnology. Although a great deal ofprogress has been made, I anticipate that future research willgreatly expand our knowledge of this archaeal group. Compre-hensive studies of chemical composition variations in mem-brane lipids and detailed protein structural-functional studieswill help in gaining a deeper insight into the mechanisms ofadaptation to low pH. The cultivation and description of newmembers, especially representatives of the Ferroplasmaceaefrom a marine milieu, will undoubtedly contribute to our un-derstanding of how these organisms were, and are, dissemi-nated across remote geographical regions isolated by oceansyet express highly similar genomic composition and possessidentical molecular taxonomy markers. Whether the oceanseabed functions as a “conveyer belt” (33) and distributesmicrobes globally, a plausible explanation for such a wide dis-tribution of Ferroplasmaceae, remains to be established. Thegenomic data on cultured and readily available strains of F.acidiphilum (YT) and A. aeolicum (VT) for the scientific com-munity will soon become available to the broader public (un-published data) and hopefully will stimulate further researchon this microbial group. It is worth remembering that theFerroplasma-based microbial community became the subject ofthe very first whole-community metagenomics study (52). Thatlandmark study was followed by a series of culture-indepen-dent genomics and proteomics studies on AMD communitiesof Iron Mountain (California), as reviewed by Denef and co-authors (14), contributing significantly to an understanding ofmicrobial diversity, dynamics, and functioning of the ecosys-tem. It is therefore likely that the emerging high-throughput“-omics’ approaches will complement the traditional reduc-tionist mechanistic studies and will further contribute to gain-ing a holistic view of the functioning of complex microbialcommunities as whole systems.

ACKNOWLEDGMENTS

This work was supported by the MetaGenoMik initiative of theFederal Ministry of Science and Education (Germany) (BMBF project0313751K) and by the EU FP7 project KBBE-2009-226977, MarineMetagenomics for New Biotechnological Applications (MAMBA).

I thank Peter Golyshin, Manuel Ferrer, Michail Yakimov, and KenTimmis for helpful discussions and comments. I am also indebted toTom DeLuca for critical reading of the manuscript.

REFERENCES

1. Allen, E. E., et al. 2007. Genome dynamics in a natural archaeal population.Proc. Natl. Acad. Sci. U. S. A. 104:1883–1888.

2. Andersson, A. F., and J. F. Banfield. 2008. Virus population dynamics andacquired virus resistance in natural microbial communities. Science 320:1047–1050.

3. Baker, B. J., and J. F. Banfield. 2003. Microbial communities in acid minedrainage. FEMS Microbiol. Ecol. 44:139–152.

4. Baker, B. J., et al. 2006. Lineages of acidophilic archaea revealed by com-munity genomic analysis. Science 314:1933–1935.

5. Baker-Austin, C., M. Dopson, M. Wexler, R. G. Sawers, and P. L. Bond.2005. Molecular insight into extreme copper resistance in the extremophilicarchaeon “Ferroplasma acidarmanus” Fer1. Microbiology 151:2637–2646.

6. Baker-Austin, C., et al. 2007. Extreme arsenic resistance by the extremo-philic archaeon “Ferroplasma acidarmanus” Fer1. Extremophiles 11:425–434.

7. Baker-Austin, C., J. Potrykus, M. Wexler, P. L. Bond, and M. Dopson. 2010.Biofilm development in the extremely acidophilic archaeon �Ferroplasmaacidarmanus’ Fer1. Extremophiles 14:485–491.

8. Batrakov, S. G., T. A. Pivovarova, S. E. Esipov, V. I. Sheichenko, and G. I.Karavaiko. 2002. Beta-D-glucopyranosyl caldarchaetidylglycerol is the mainlipid of the acidophilic, mesophilic, ferrous iron-oxidising archaeon Ferro-plasma acidiphilum. Biochim. Biophys. Acta 1581:29–35.

9. Baumler, D. J., K. C. Jeong, B. G. Fox, J. F. Banfield, and C. W. Kaspar.2005. Sulfate requirement for heterotrophic growth of “Ferroplasma acidar-manus” strain fer1. Res. Microbiol. 156:492–498.

10. Baumler, D. J., K. F. Hung, K. C. Jeong, and C. W. Kaspar. 2007. Productionof methanethiol and volatile sulfur compounds by the archaeon “Ferro-plasma acidarmanus”. Extremophiles 11:841–851.

11. Bruneel, O., et al. 2008. Archaeal diversity in Fe-As rich acid mine drainageat Carnoules (France). Extremophiles 12:563–571.

12. Bryan, C., K. B. Hallberg, and D. B. Johnson. 2006. Mobilization of metalsin mineral tailings at the abandoned Sao Domingos copper mine (Portugal)by indigenous acidophilic bacteria. Hydrometallurgy 83:184–194.

13. Comolli, L. R., B. J. Baker, K. H. Downing, C. E. Siegerist, and J. F.Banfield. 2009. Three-dimensional analysis of the structure and ecology of anovel, ultra-small archaeon. ISME J. 3:159–167.

14. Denef, V. J., R. S. Mueller, and J. F. Banfield. 2010. AMD biofilms: usingmodel communities to study microbial evolution and ecological complexityin nature. ISME J. 4:599–610.

15. Dick, G. J. et al. 2009. Community-wide analysis of microbial genome se-quence signatures. Genome Biology 10:R85.

16. Dopson, M., C. Baker-Austin, A. Hind, J. P. Bowman, and P. L. Bond. 2004.Characterization of Ferroplasma isolates and Ferroplasma acidarmanus sp.nov., extreme acidophiles from acid mine drainage and industrial bioleachingenvironments. Appl. Environ. Microbiol. 70:2079–2088.

17. Dopson, M., C. Baker-Austin, and P. L. Bond. 2005. Analysis of differentprotein expression during growth states of Ferroplasma strains and insightsinto electron transport for iron oxidation. Microbiology 151:4127–4137.

18. Edwards, K. J., P. L. Bond, T. M. Gihring, and J. F. Banfield. 2000. Anarchaeal iron-oxidizing extreme acidophile important in acid mine drainage.Science 287:1796–1799.

19. Farahat, M., T. Hirajima, and K. Sasaki. 2010. Adhesion of Ferroplasmaacidiphilum onto pyrite calculated from the extended DLVO theory usingthe van Oss-Good-Chaudhury approach. J. Colloid. Interface Sci. 349:594–601.

20. Ferrer, M., O. V. Golyshina, A. Beloqui, P. N. Golyshin, and K. N. Timmis.2007. The cellular machinery of Ferroplasma acidiphilum is iron-protein-dominated. Nature 445:91–94.

21. Ferrer, M. et al. 2008. A purple acidophilic di-ferric DNA ligase fromFerroplasma. Proc. Natl. Acad. Sci. U. S. A. 105:8878–8883.

22. Gao, B., and R. S. Gupta. 2007. Phylogenomic analysis of proteins that aredistinctive of Archaea and its main subgroups and the origin of methano-genesis. BMC Genomics 8:86.

23. Garcia-Moyano, A., E. Gonzalez-Toril, A. Aguilera, and R. Amils. 2007.Prokaryotic community composition and ecology of floating macroscopicfilaments from an extreme acidic environment, Rio Tinto (SW, Spain). Syst.Appl. Microbiol. 30:601–614.

24. Garrido, P. et al. 2008. An oligonucleotide prokaryotic acidophile microar-ray: its validation and its use to monitor seasonal variations in extreme acidicenvironments with total environmental RNA. Environ. Microbiol. 10:836–850.

25. Golyshina, O. V., et al. 2000. Ferroplasma acidiphilum gen. nov. sp. nov., anacidophilic, autotrophic, ferrous-iron-oxidizing, cell-wall-lacking, mesophilicmember of the Ferroplasmaceae fam. nov., comprising a distinct lineage ofthe Archaea. Int. J. Syst. Evol. Microbiol. 50:997–1006.

26. Golyshina, O. V., and K. N. Timmis. 2005. Ferroplasma and relatives, re-cently discovered cell-wall-lacking archaea making a living in extremely acid,heavy metal-rich environments. Environ. Microbiol. 7:1277–1288.

27. Golyshina, O. V., P. N. Golyshin, K. N. Timmis, and M. Ferrer. 2006. The



.asm.org/

Dow

nloaded from

http://aem.asm.org/

“pH optimum anomaly” of intracellular enzymes of Ferroplasma acidiphilum.Environ. Microbiol. 8:416–425.

28. Golyshina, O. V., et al. 2009. Acidiplasma aeolicum gen. nov. sp. nov., a noveleuryarchaeon of the family Ferroplasmaceae isolated from a hydrothermalpool, and transfer of Ferroplasma cupricumulans to Acidiplasma cupricumu-lans comb. nov. Int. J. Syst. Evol. Microbiol. 59:2815–2823.

29. Gonzalez-Toril, E., E. Llobet-Brossa, E. O. Casamayor, R. Amann, and R.Amils. 2003. Microbial ecology of an extreme acidic environment, the TintoRiver. Appl. Environ. Microbiol. 69:4853–4865.

30. Hawkes, R. B., P. D. Franzmann, G. O’Hara, and J. J. Plumb. 2006. Ferro-plasma cupricumulans sp. nov., a novel moderately thermophilic, acidophilicarchaeon isolated from an industrial-scale chalcocite bioleach heap. Ex-tremophiles 10:525–530.

31. Hawkes, R. B., P. D. Franzmann, G. O’Hara, and J. J. Plumb. 2008. List ofnew names and new combinations previously effectively, but not validly,published, validation list no. 119, Ferroplasma cupricumulans sp. nov. Int. J.Syst. Evol. Microbiol. 58:1–2.

32. Johnson, D. B. 2009. Extremophiles: acidic environments, p. 107–126. In M.Schaechter (ed.), Encyclopaedia of microbiology. Elsevier, Oxford, UnitedKingdom.

33. Jørgensen, B. B., and A. Boetius. 2007. Feast and famine—microbial life inthe deep-sea bed. Nat. Rev. Microbiol. 5:770–781.

34. Karavaiko, G. I., G. A. Dubinina, and T. F. Kondrat’eva. 2006. Lithotrophicmicroorganisms of the oxidative cycles of sulfur and iron. Microbiology75:512–545.

35. Kondrat’eva, T. F., T. A. Pivovarova, L. N. Muntyan, S. N. Ageeva, and G. I.Karavaiko. 2003. The strain genotypic heterogeneity of chemolithotrophicmicroorganisms, p. 1379–1388. In Proc. 15th Int. Biohydrometallurgy Symp.,Athens, Greece, 14 to 19 September 2003.

36. Konings, W. N., S-.V. Albers, S. Koning, and A. J. M. Driessen. 2002. Thecell membrane plays a crucial role in survival of bacteria and archaea inextreme environments. Antonie Van Leeuwenhoek 81:61–72.

37. Lomans, B. P., et al. 2001. Microbial population involved in cycling ofdimethyl sulfide and methanethiol in freshwater sediments. Appl. Environ.Microbiol. 67:1044–1051.

38. Macalady, J. L., D. S. Jones, and E. H. Lyon. 2007. Extremely acidic, pen-dulous cave wall biofilms from the Frasassi cave system, Italy. Environ.Microbiol. 9:1402–1414.

39. Nakatani, M., S. Ezaki, H. Atomi, and T. Imanaka. 2000. DNA ligase froma hyperthermophilic archaeon with unique cofactor specificity. J. Bacteriol.182:6424–6433.

40. Okibe, N., M. Gericke, K. B. Hallberg, and D. B. Johnson. 2003. Enumer-ation and characterization of acidophilic microorganisms isolated from apilot plant stirred tank bioleaching operation. Appl. Environ. Microbiol.69:1936–1943.

41. Pivovarova, T. A., et al. 2002. Phenotypic features of Ferroplasma acidiphilumstrains YT and Y-2. Microbiology 71:809–818.

42. Potrykus, J., V. R. Jonna, and M. Dopson. 2011. Iron homeostasis andresponses to iron limitation in extreme acidophiles from the Ferroplasmagenus. Proteomics 11:52–63.

43. Prangishvili, D., P. Forterre, and R. A. Garrett. 2006. Viruses of the Ar-chaea: unifying view. Nat. Rev. Microbiol. 4:837–848.

44. Pugh, R. A. et al. 2008. The iron-containing domain is essential in Rad3helicases for coupling of ATP hydrolysis to DNA translocation and fortargeting the helicase to the single-stranded DNA-double-stranded DNAjunction. J. Biol. Chem. 283:1732–1743.

45. Qiu, G. Z. et al. 2008. Archaeal diversity in acid mine drainage from Da-baoshan Mine, China. J. Basic Microbiol. 48:401–409.

46. Remonsellez, F., et al. 2009. Dynamic of active microorganisms inhabiting abioleaching industrial heap of low-grade copper sulfide ore monitored byreal-time PCR and oligonucleotide prokaryotic acidophile microarray. Mi-crob. Biotechnol. 2:613–624.

47. Rohwer, F., D. Prangishvili, and D. Lindell. 2009. Role of viruses in theenvironment. Environ. Microbiol. 11:2771–2774.

48. Rolland, J.-L., Y. Gueguen, C. Persillon, J.-M. Masson, and J. Dietrich.2004. Characterization of a thermophilic DNA ligase from the archaeonThermococcus fumicolans. FEMS Microbiol. Lett. 236:267–273.

49. Schleper, C. et al. 1995. Picrophilus gen. nov., fam. nov.: a novel aerobic,heterotrophic, thermoacidophilic genus and family comprising archaea ca-pable of growth around pH 0. J. Bacteriol. 177:7050–7059.

50. Schleper, C., G. Puhler, H.-P. Klenk, and W. Zillig. 1996. Picrophilus oshi-mae and Picrophilus torridus fam. nov., gen. nov., sp. nov., two species ofhyperacidophilic, thermophilic, heterotrophic, aerobic archaea. Int. J. Syst.Bacteriol. 46:814–816.

51. Tan, G. L., et al. 2008. Culturable and molecular phylogenetic diversity ofmicroorganisms in an open-dumped, extremely acidic Pb/Zn mine tailings.Extremophiles 12:657–664.

52. Tyson, G. W. et al. 2004. Community structure and metabolism throughreconstruction of microbial genomes from the environment. Nature 428:37–43.

53. Valentine, D. L. 2007. Adaptations to energy stress dictate the ecology andevolution of the Archaea. Nat. Rev. Microbiol. 5:316–323.

54. van de Vossenberg, J. L., A. J. Driessen, W. Zillig, and W. N. Konings. 1998.Bioenergetics and cytoplasmic membrane stability of the extremely acido-philic, thermophilic archaeon Picrophilus oshimae. Extremophiles 2:67–74.

55. Xiao, S., X. Xie, J. Liu, Z. He, and Y. Hu. 2008. Compositions and structuresof archaeal communities in acid mineral bioleaching systems of DongxiangCopper Mine and Yinshan Lead-Zinc Mine, China. Curr. Microbiol. 57:239–244.

56. Xiao, S., X. Xie, and J. Liu. 2009. Microbial communities in acid waterenvironments of two mines, China. Environ. Pollut. 157:1045–1050.

57. Xie, X., S. Xiao, Z. He, J. Liu, and G. Qiu. 2007. Microbial populations inacid mineral bioleaching systems of Tong Shankou Copper Mine, China.J. Appl. Microbiol. 103:1227–1238.

58. Zhang, R. B. et al. 2009. Application of real-time PCR to monitor populationdynamics of defined mixed cultures of moderate thermophiles involved inbioleaching of chalcopyrite. Appl. Microbiol. Biotechnol. 81:1161–1168.

59. Zhou, H. et al. 2008. Isolation and characterization of Ferroplasma thermo-philum sp. nov., a novel extremely acidophilic, moderately thermophilicarchaeon and its role in bioleaching of chalcopyrite. J. Appl. Microbiol.105:591–601.



.asm.org/

Dow

nloaded from

http://aem.asm.org/

environmental, biogeographic, and biochemical …aem.asm.org/content/77/15/5071.full.pdfing their...

Documents