Microbial Mat Communities Research Articles

Bacterial and Archaeal Diversity in Hypersaline Cyanobacterial Mats Along a Transect in the Intertidal Flats of the Sultanate of Oman.

Hypersaline intertidal zones are highly dynamic ecosystems that are exposed to multiple extreme environmental conditions including rapidly and frequently changing parameters (water, nutrients, temperature) as well as highly elevated salinity levels often caused by high temperatures and evaporation rates. Microbial mats in most extreme settings, as found at the coastline of the subtropical-arid Arabian Peninsula, have been relatively less studied compared to their counterparts around the world. We report, here, for the first time on the diversity of the bacterial and archaeal communities of marine microbial mats along an intertidal transect in a wide salt flat with strongly increased salinity employing Illumina MiSeq technology for amplicon sequencing of 16S rRNA gene fragments. Microbial communities were dominated by typical halotolerant to halophilic microorganisms, with clear shifts in community composition, richness, and diversity along the transect. Highly adapted specialists (e.g., Euhalothece, Salinibacter, Nanohaloarchaeota) were mainly found at the most extreme, upper tidal sites and less specialized organisms with wide tolerance ranges (e.g., Lyngbya, Rhodovibrio, Salisaeta, Halobacteria) in intermediate sites of the transect. The dominating taxa in the lower tidal sites were typical members of well-stabilized mats (e.g., Coleofasciculus, Anaerolineaceae, Thaumarchaeota). Up to 40% of the archaeal sequences per sample represented so far unknown phyla. In conclusion, the bacterial richness and diversity increased from upper towards lower tidal sites in line with increasing mat stabilization and functional diversity, opposed to that of cyanobacteria only and archaea, which showed their highest richness and diversity in upper tidal samples.

Comparison of two bioinformatics tools used to characterize the microbial diversity and predictive functional attributes of microbial mats from Lake Obersee, Antarctica

In this study, using NextGen sequencing of the collective 16S rRNA genes obtained from two sets of samples collected from Lake Obersee, Antarctica, we compared and contrasted two bioinformatics tools, PICRUSt and Tax4Fun. We then developed an R script to assess the taxonomic and predictive functional profiles of the microbial communities within the samples. Taxa such as Pseudoxanthomonas, Planctomycetaceae, Cyanobacteria Subsection III, Nitrosomonadaceae, Leptothrix, and Rhodobacter were exclusively identified by Tax4Fun that uses SILVA database; whereas PICRUSt that uses Greengenes database uniquely identified Pirellulaceae, Gemmatimonadetes A1-B1, Pseudanabaena, Salinibacterium and Sinobacteraceae. Predictive functional profiling of the microbial communities using Tax4Fun and PICRUSt separately revealed common metabolic capabilities, while also showing specific functional IDs not shared between the two approaches. Combining these functional predictions using a customized R script revealed a more inclusive metabolic profile, such as hydrolases, oxidoreductases, transferases; enzymes involved in carbohydrate and amino acid metabolisms; and membrane transport proteins known for nutrient uptake from the surrounding environment. Our results present the first molecular-phylogenetic characterization and predictive functional profiles of the microbial mat communities in Lake Obersee, while demonstrating the efficacy of combining both the taxonomic assignment information and functional IDs using the R script created in this study for a more streamlined evaluation of predictive functional profiles of microbial communities.

The Dark Side of the Mushroom Spring Microbial Mat: Life in the Shadow of Chlorophototrophs. II. Metabolic Functions of Abundant Community Members Predicted from Metagenomic Analyses.

Microbial mat communities in the effluent channels of Octopus and Mushroom Springs within the Lower Geyser Basin of Yellowstone National Park have been extensively characterized. Previous studies have focused on the chlorophototrophic organisms of the phyla Cyanobacteria and Chloroflexi. However, the diversity and metabolic functions of the other portion of the community in the microoxic/anoxic region of the mat are poorly understood. We recently described the diverse but extremely uneven microbial assemblage in the undermat of Mushroom Spring based on 16S rRNA amplicon sequences, which was dominated by Roseiflexus members, filamentous anoxygenic chlorophototrophs. In this study, we analyzed the orange-colored undermat portion of the community of Mushroom Spring mats in a genome-centric approach and discuss the metabolic potentials of the major members. Metagenome binning recovered partial genomes of all abundant community members, ranging in completeness from ~28 to 96%, and allowed affiliation of function with taxonomic identity even for representatives of novel and Candidate phyla. Less complete metagenomic bins correlated with high microdiversity. The undermat portion of the community was found to be a mixture of phototrophic and chemotrophic organisms, which use bicarbonate as well as organic carbon sources derived from different cell components and fermentation products. The presence of rhodopsin genes in many taxa strengthens the hypothesis that light energy is of major importance. Evidence for the usage of all four bacterial carbon fixation pathways was found in the metagenome. Nitrogen fixation appears to be limited to Synechococcus spp. in the upper mat layer and Thermodesulfovibrio sp. in the undermat, and nitrate/nitrite metabolism was limited. A closed sulfur cycle is indicated by biological sulfate reduction combined with the presence of genes for sulfide oxidation mainly in phototrophs. Finally, a variety of undermat microorganisms have genes for hydrogen production and consumption, which leads to the observed diel hydrogen concentration patterns.

Ferrous iron- and ammonium-rich diffuse vents support habitat-specific communities in a shallow hydrothermal field off the Basiluzzo Islet (Aeolian Volcanic Archipelago).

Ammonium- and Fe(II)-rich fluid flows, known from deep-sea hydrothermal systems, have been extensively studied in the last decades and are considered as sites with high microbial diversity and activity. Their shallow-submarine counterparts, despite their easier accessibility, have so far been under-investigated, and as a consequence, much less is known about microbial communities inhabiting these ecosystems. A field of shallow expulsion of hydrothermal fluids has been discovered at depths of 170-400meters off the base of the Basiluzzo Islet (Aeolian Volcanic Archipelago, Southern Tyrrhenian Sea). This area consists predominantly of both actively diffusing and inactive 1-3 meters-high structures in the form of vertical pinnacles, steeples and mounds covered by a thick orange to brown crust deposits hosting rich benthic fauna. Integrated morphological, mineralogical, and geochemical analyses revealed that, above all, these crusts are formed by ferrihydrite-type Fe3+ oxyhydroxides. Two cruises in 2013 allowed us to monitor and sampled this novel ecosystem, certainly interesting in terms of shallow-water iron-rich site. The main objective of this work was to characterize the composition of extant communities of iron microbial mats in relation to the environmental setting and the observed patterns of macrofaunal colonization. We demonstrated that iron-rich deposits contain complex and stratified microbial communities with a high proportion of prokaryotes akin to ammonium- and iron-oxidizing chemoautotrophs, belonging to Thaumarchaeota, Nitrospira, and Zetaproteobacteria. Colonizers of iron-rich mounds, while composed of the common macrobenthic grazers, predators, filter-feeders, and tube-dwellers with no representatives of vent endemic fauna, differed from the surrounding populations. Thus, it is very likely that reduced electron donors (Fe2+ and NH4+ ) are important energy sources in supporting primary production in microbial mats, which form a habitat-specific trophic base of the whole Basiluzzo hydrothermal ecosystem, including macrobenthic fauna.

The vesicomyid bivalve habitat at cold seeps supports heterogeneous and dynamic macrofaunal assemblages

The high biodiversity found at cold seeps, despite elevated concentrations of methane and hydrogen sulfide, is attributed to multiple sources of habitat heterogeneity. In addition to geological and geochemical processes, biogenic habitats formed by large symbiont-bearing taxa, such as bivalves and siboglinid tubeworms, or by microbial mats drive the biodiversity of small-sized fauna. However, because these habitat-forming species also depend on geochemical gradients, the respective influence of abiotic and biotic factors in structuring associated macrofaunal communities is often unresolved. The giant pockmark Regab located at 3200m depth on the Congo margin is characterized by different fluid-flow regimes, providing a mosaic of the most common biogenic habitats encountered at seeps: microbial mats, mussel beds, and vesicomyid clam beds; the latter being distributed along a gradient of environmental conditions from the center to the periphery of the pockmark. Here, we examined the structure of macrofaunal communities in biogenic habitats formed in soft sediment to (1) determine the influence of the habitats on the associated macrofaunal communities (inter-habitat comparison), (2) describe how macrofaunal communities vary among vesicomyid clam beds (intra-habitat comparison) and (3) assess the inter-annual variation in vesicomyid beds based on repeated sampling at a three-year interval. The highest densities were found in the microbial mat communities in intermediate fluid-flow areas, but they had low diversity — also observed in the sediment close to mussel beds. In contrast, vesicomyid beds harbored the highest diversity. The vesicomyid beds did not show a homogeneous macrofaunal community across sampled areas; instead, density and composition of macrofauna varied according to the location of the beds inside the pockmark. The clam bed sampled in the most active, central part of the pockmark resembled bacterial mat communities by the presence of highly sulfide-tolerant species living at the sediment surface, along with vesicomyid juveniles. This similarity suggests a gradual change in community composition from mats to clam beds. Inter-annual comparisons of the different clam beds highlighted that the most active central site had a more variable community than its peripheral counterparts. Finally, a rapid shift in community structure, particularly in polychaete families, in experimentally reduced oxygen concentrations in the central part of Regab, suggests that high beta-diversity communities can withstand intense variation in geochemical conditions. These community dynamics are likely related to the diversity and to the plasticity of the vesicomyids themselves, because they can cope with high spatial and temporal environmental variability at a very local scale.

Biogeochemistry of intertidal microbial mats from Qatar: New insights from organic matter characterisation

Understanding early organic matter (OM) alteration and preservation in marine carbonate-evaporite systems could improve understanding of carbon cycling and hydrocarbon source rock prediction in such environments. It is possible that organic-rich microbial mats are important contributors to preserved hydrocarbons and, to explore this, we examined changes in lipid composition in such a mat from a mesohaline intertidal lagoon, eastern Qatar. The mat reaches>5cm thickness over a carbonate mud substrate, rich in seagrass, gastropods and other small bioclasts. Clear lamination, with distinct downward colour changes from green to pink to brown, reflects different microbial mat communities. The layers contain spheroids of probable dolomite, the precipitation of which was plausibly bacterially-mediated. Lipids [n-alkanes, fatty acids (FAs), hopanoids, isoprenoid hydrocarbons, dialkyl glycerol diethers (DAGEs), and isoprenoid (0–4) and branched (Ia–IIIa) GDGTs] reflected the diverse mat-building phototrophic, heterotrophic and chemoorganotrophic microorganisms, as well as some likely allochthonous material (i.e. steroids, n-alkanols, high molecular weight n-alkanes). The lipids clearly documented the change in microbial community, with phytene(s) being the predominant hydrocarbon in the phototrophic surface layer. O2 and pH dropped significantly 0.2cm below the mat surface, coincident with the predominance of Deltaproteobacteria and increased concentrations of archaeal and bacterial glycerol dialkyl glycerol tetraether lipids and C15/C16 and C16/C17 dialkyl glycerol ether lipids in the deeper layers. Archaeol, likely of methanogen origin, was most abundant in the deepest layer. Allochthonous inputs occurred throughout the mat, including abundant steroids, especially dinosterol and dinostanol, possibly related to periodic algal (dinoflagellate) blooms in the Arabian Gulf. Both n-alkanes and n-alkanols appeared to be derived from seagrass. OM content decreased in the deepest mat; this suggests an overall low preservation potential of OM in intertidal mesohaline-hypersaline mats of the Arabian Gulf, which in turn suggests that these are not the major source of hydrocarbons in microbially-dominated carbonate-evaporite systems.

Characterization of Chemosynthetic Microbial Mats Associated with Intertidal Hydrothermal Sulfur Vents in White Point, San Pedro, CA, USA.

The shallow-sea hydrothermal vents at White Point (WP) in Palos Verdes on the southern California coast support microbial mats and provide easily accessed settings in which to study chemolithoautotrophic sulfur cycling. Previous studies have cultured sulfur-oxidizing bacteria from the WP mats; however, almost nothing is known about the in situ diversity and activity of the microorganisms in these habitats. We studied the diversity, micron-scale spatial associations and metabolic activity of the mat community via sequence analysis of 16S rRNA and aprA genes, fluorescence in situ hybridization (FISH) microscopy and sulfate reduction rate (SRR) measurements. Sequence analysis revealed a diverse group of bacteria, dominated by sulfur cycling gamma-, epsilon-, and deltaproteobacterial lineages such as Marithrix, Sulfurovum, and Desulfuromusa. FISH microscopy suggests a close physical association between sulfur-oxidizing and sulfur-reducing genotypes, while radiotracer studies showed low, but detectable, SRR. Comparative 16S rRNA gene sequence analyses indicate the WP sulfur vent microbial mat community is similar, but distinct from other hydrothermal vent communities representing a range of biotopes and lithologic settings. These findings suggest a complete biological sulfur cycle is operating in the WP mat ecosystem mediated by diverse bacterial lineages, with some similarity with deep-sea hydrothermal vent communities.

Diverse sulfur metabolisms from two subterranean sulfidic spring systems.

In sulfidic environments, microbes oxidize reduced sulfur compounds via several pathways. We used metagenomics to investigate sulfur metabolic pathways from microbial mat communities in two subterranean sulfidic streams in Lower Kane Cave, WY, USA and from Glenwood Hot Springs, CO, USA. Both unassembled and targeted recA gene assembly analyses revealed that these streams were dominated by Epsilonproteobacteria and Gammaproteobacteria, including groups related to Sulfurovum, Sulfurospirillum, Thiothrix and an epsilonproteobacterial group with no close cultured relatives. Genes encoding sulfide:quinone oxidoreductase (SQR) were abundant at all sites, but the specific SQR type and the taxonomic affiliation of each type differed between sites. The abundance of thiosulfate oxidation pathway genes (Sox) was not consistent between sites, although overall they were less abundant than SQR genes. Furthermore, the Sox pathway appeared to be incomplete in all samples. This work reveals both variations in sulfur metabolism within and between taxonomic groups found in these systems, and the presence of novel epsilonproteobacterial groups.

The Dark Side of the Mushroom Spring Microbial Mat: Life in the Shadow of Chlorophototrophs. I. Microbial Diversity Based on 16S rRNA Gene Amplicons and Metagenomic Sequencing.

Microbial-mat communities in the effluent channels of Octopus and Mushroom Springs within the Lower Geyser Basin at Yellowstone National Park have been studied for nearly 50 years. The emphasis has mostly focused on the chlorophototrophic bacterial organisms of the phyla Cyanobacteria and Chloroflexi. In contrast, the diversity and metabolic functions of the heterotrophic community in the microoxic/anoxic region of the mat are not well understood. In this study we analyzed the orange-colored undermat of the microbial community of Mushroom Spring using metagenomic and rRNA-amplicon (iTag) analyses. Our analyses disclosed a highly diverse community exhibiting a high degree of unevenness, strongly dominated by a single taxon, the filamentous anoxygenic phototroph, Roseiflexus spp. The second most abundant organisms belonged to the Thermotogae, which have been hypothesized to be a major source of H2 from fermentation that could enable photomixotrophic metabolism by Chloroflexus and Roseiflexus spp. Other abundant organisms include two members of the Armatimonadetes (OP10); Thermocrinis sp.; and phototrophic and heterotrophic members of the Chloroflexi. Further, an Atribacteria (OP9/JS1) member; a sulfate-reducing Thermodesulfovibrio sp.; a Planctomycetes member; a member of the EM3 group tentatively affiliated with the Thermotogae, as well as a putative member of the Arminicenantes (OP8) represented ≥1% of the reads. Archaea were not abundant in the iTag analysis, and no metagenomic bin representing an archaeon was identified. A high microdiversity of 16S rRNA gene sequences was identified for the dominant taxon, Roseiflexus spp. Previous studies demonstrated that highly similar Synechococcus variants in the upper layer of the mats represent ecological species populations with specific ecological adaptations. This study suggests that similar putative ecotypes specifically adapted to different niches occur within the undermat community, particularly for Roseiflexus spp.

Palaeoredox geochemistry and bioturbation levels of the exceptionally preserved early Cambrian Indian Springs biota, Nevada, USA

The Sirius Passet Lagerstatte (SP), Peary Land, North Greenland, occurs in black slates deposited at or just below storm wave base. It represents the earliest Cambrian microbial mat community with exceptional preservation, predating the Burgess Shale by 10 million years. Trilobites from the SP are preserved as complete, three-dimensional, concave hyporelief external moulds and convex epirelief casts. External moulds are shown to consist of a thin veneer of authigenic silica. The casts are formed from silicified cyanobacterial mat material. Silicification in both cases occurred shortly after death within benthic cyanobacterial mats. Pore waters were alkali, silica-saturated, high in ferric iron but low in oxygen and sulphate. Excess silica was likely derived from remobilized biogenic silica. The remarkable siliceous death mask preservation opens a new window on the environment and location of the Cambrian Explosion. This window closed with the appearance of abundant mat grazers later as the Cambrian Explosion intensified.

Comparative Genomics and Functional Analysis of Carbohydrate Utilization Networks in Unicyanobacterial Consortia Derived from Hypersaline Lake Microbial Mats

Hot Lake is a meromictic, hypersaline lake located in Washington state, USA. It harbors a phototrophic microbial mat community stable in dramatic seasonal environmental changes. The complexity of natural community hinders to analyze metabolic interactions between its members. To manage this obstacle, unicyanobacterial consortia (UCC) were sampled from the community and sequenced. UCC is a microbial community in which one cyanobacterium serves as the sole primary producer of carbon sources to several heterotrophic bacteria.Recently available metagenomes for two UCC revealed a shared set of 19 microbial operational taxonomic units (OTU), whose individual genomes were reconstructed by co‐assembly and abundance profile binning. We used this genomic data and a comparative genomics approach to infer carbohydrate utilization pathways and their transcription regulation.We scanned all UCC proteomes against the KEGG Orthology, Pfam, GO and SEED databases to reveal genes potentially involved in sugar utilization. Then we analyzed the genomic and functional contexts of gene loci encoding the obtained proteins and reconstructed the respective metabolic pathways and transcriptional regulons.As result, we observed catabolic pathways for 32 various carbohydrates and their derivatives. Distribution of the inferred catabolic pathways has highly mosaic structure across the UCC genomes. The largest number of pathways was observed in two representatives of the Halomonas genus (14–15 pathways) and one Rhodobacteriaceae sp. (15 pathways). In other UCC genomes, we found up to 10 carbohydrate utilization pathways per genome. However in 7 genomes we didn't observe any pathway. The most widely distributed pathways in UCC were the alpha‐glucosides and the DeLey‐Doudoroff galactose utilization pathways. Both were found in 7 genomes. Majority of pathways are distributed among 1–3 genomes. The reconstructed catabolic pathways were partially validated by phenotypic analyses of UCC community members that were isolated in a pure culture.In the Rhodobacteriaceae sp., we found a novel catabolic pathway that was proposed to be involved in mannoheptulose utilization. To our knowledge, the proposed mannoheptulose catabolic pathway is the first case of a pathway for heptose utilization and will require further experimental validation.The identified pathways are potentially regulated by local transcription factors (TFs) that are often co‐localized with the respective sugar catabolic gene loci. For 63 out of the 80 identified TFs we identified their cognate DNA binding motifs and reconstructed regulons using the bioinformatics approach.Support or Funding InformationThis research was supported by the Genomic Science Program (GSP), Office of Biological and Environmental Research (OBER), and U.S. Department of Energy (DOE) and is a contribution of the Pacific Northwest National Laboratory (PNNL) Foundational Scientific Focus Area.

Mineralogy and Microbial Diversity of the Microbialites in the Hypersaline Storr's Lake, the Bahamas.

Microbialites found in the low-light-intensity, hypersaline waters of Storr's Lake (SL), San Salvador Island, the Bahamas, were investigated with respect to their morphology, mineralogy, and microbial diversity. Previously described microbialite morphologies, as well as a newly identified "multi-cuspate" morphology, were observed at various depths. Electron microscopy analysis revealed the presence of angular, blocky, and needle-shaped crystals with mineralized cyanobacterial filaments and remains of exopolymeric substances. X-ray diffraction studies confirmed the presence of both Mg-calcite and aragonite in the plateau-mushroom and pinnacle mound microbialites, whereas only Mg-calcite was identified in the other microbialite morphotypes. A comprehensive molecular analysis using barcoded pyrosequencing of five different microbial mat communities identified at least 12 dominant bacterial phyla. Cyanobacteria were generally low in abundance and ranged from ∼0.01% in the deeper pinnacle mounds to ∼3.2% in the shallow calcareous knobs. Other photosynthetic members included green nonsulfur bacteria of the phylum Chloroflexi and purple sulfur bacteria of the class Gammaproteobacteria. All mat types contained significant amounts of sulfate-reducing and dehalogenating bacteria. The low light intensity reaching the deeper microbialites, the lack of dominant cyanobacteria, and the abundance of sulfate reducers and Chloroflexi collectively suggest that sulfate reduction and anoxygenic photosynthetic processes influence the carbonate biomineralization process in these systems.

An Unusual Inverted Saline Microbial Mat Community in an Interdune Sabkha in the Rub' al Khali (the Empty Quarter), United Arab Emirates

Salt flats (sabkha) are a recognized habitat for microbial life in desert environments and as analogs of habitats for possible life on Mars. Here we report on the physical setting and microbiology of interdune sabkhas among the large dunes in the Rub' al Khali (the Empty Quarter) in Liwa Oasis, United Arab Emirates. The salt flats, composed of gypsum and halite, are moistened by relatively fresh ground water. The result is a salinity gradient that is inverted compared to most salt flat communities with the hypersaline layer at the top and freshwater layers below. We describe and characterize a rich photosynthetically-based microbial ecosystem that is protected from the arid outside environment by a translucent salt crust. Gases collected from sediments under shallow ponds in the sabkha contain methane in concentrations as high as 3400 ppm. The salt crust could preserve biomarkers and other evidence for life in the salt after it dries out. Chloride-filled depressions have been identified on Mars and although surface flow of water is unlikely on Mars today, ground water is possible. Such a near surface system with modern groundwater flowing under ancient salt deposits could be present on Mars and could be accessed by surface rovers.

Assembly and Succession of Iron Oxide Microbial Mat Communities in Acidic Geothermal Springs.

Biomineralized ferric oxide microbial mats are ubiquitous features on Earth, are common in hot springs of Yellowstone National Park (YNP, WY, USA), and form due to direct interaction between microbial and physicochemical processes. The overall goal of this study was to determine the contribution of different community members to the assembly and succession of acidic high-temperature Fe(III)-oxide mat ecosystems. Spatial and temporal changes in Fe(III)-oxide accretion and the abundance of relevant community members were monitored over 70 days using sterile glass microscope slides incubated in the outflow channels of two acidic geothermal springs (pH = 3–3.5; temperature = 68–75°C) in YNP. Hydrogenobaculum spp. were the most abundant taxon identified during early successional stages (4–40 days), and have been shown to oxidize arsenite, sulfide, and hydrogen coupled to oxygen reduction. Iron-oxidizing populations of Metallosphaera yellowstonensis were detected within 4 days, and reached steady-state levels within 14–30 days, corresponding to visible Fe(III)-oxide accretion. Heterotrophic archaea colonized near 30 days, and emerged as the dominant functional guild after 70 days and in mature Fe(III)-oxide mats (1–2 cm thick). First-order rate constants of Fe(III)-oxide accretion ranged from 0.046 to 0.05 day−1, and in situ microelectrode measurements showed that the oxidation of Fe(II) is limited by the diffusion of O2 into the Fe(III)-oxide mat. The formation of microterracettes also implicated O2 as a major variable controlling microbial growth and subsequent mat morphology. The assembly and succession of Fe(III)-oxide mat communities follows a repeatable pattern of colonization by lithoautotrophic organisms, and the subsequent growth of diverse organoheterotrophs. The unique geochemical signatures and micromorphology of extant biomineralized Fe(III)-oxide mats are also useful for understanding other Fe(II)-oxidizing systems.

Editorial: Systems Biology and Ecology of Microbial Mat Communities.

The goals of systems biology and microbial ecology are to gain a predictive understanding of how microbial communities function in dynamic systems, inclusive of interactions among community members and spatiotemporal changes in the physicochemical environment. Microorganisms in natural systems experience cycles of environmental change over different periodicities and amplitudes, and these processes are reflected in the composition, genetic repertoire and activity of microbial community members, and community function as a whole. A primary emphasis of this research topic was to focus on reports of tractable microbial communities in extreme environments (e.g., temperature, salinity, light, pH) where a foundation of genome sequence and other molecular (-omic) and geochemical measurements provide evidence of specific functional attributes of individual community members, which are directly linked with spatiotemporal changes in key environmental variables as well as the metabolic dynamics of other community members. Thermal or saline microbial mats are often stratified with respect to key environmental variables (e.g., light, oxygen) and exhibit compositional simplicity and low heterogeneity relative to habitats such as soils and/or natural waters. Consequently, the majority of contributions to this research topic focus on either high-temperature chemotrophic microbial mats, high-temperature phototrophic mats, or hypersaline phototrophic mats in marine or epsomitic systems. The structure and function of high-temperature systems of Yellowstone National Park (YNP) was evaluated using metagenome sequence and geochemical observations across a wide range of environmental conditions, which provided a basis for understanding the distribution of thermophiles in YNP and led to the discovery of several new archaeal and bacterial lineages. Genome sequences of relevant ecotypes have provided a foundation for interrogating more detailed spatiotemporal aspects of thermophilic phototrophic communities, including microsensor analysis of their physical and chemical microenvironment, and provided a rationale for comparison to hypersaline phototrophic mats. The fixation of carbon dioxide as a primary carbon source and the production of key cofactors by autotrophs are important processes, which support diverse heterotrophs across widely different environmental circumstances. Specific metabolic linkages among community members (e.g., production of storage compounds, nitrogen fixation, fermentation, sulfate reduction, hydrogen, and vitamin production) were documented in phototrophic mats, which revealed that these processes changed in unexpected ways across a diel cycle. The tight metabolic coupling among specific populations that are highly adapted to spatial and/or temporal conditions is a common theme in natural environments, and this was demonstrated in detail using different light-adapted ecotypes of cyanobacteria (Synechococcus spp.) present in alkaline siliceous geothermal mats as primary producers. Finally, controlled experiments using pure cultures and/or consortia as “systems” revealed the importance of specific nutrient requirements, and importantly, how the exoproteome of a bacterium is controlled by the level of cellular oxidation. Ultimately, a predictive understanding of the complex network of abiotic and biotic interactions that occur in natural systems will also require detailed knowledge of the regulatory and physicochemical processes that govern gene expression, post-translational modifications, and protein activity. It is our hope that the articles included in this research topic advance a more comprehensive understanding of natural microbial communities, and demonstrate the utility of coupling molecular methods with detailed spatiotemporal measurements and dissection of microbial community function across gradients in key environmental variables such as light, temperature, pH, oxygen, or hydrogen. Integrated approaches across relevant microbial scales will lead to predictive capabilities useful for engineering microbial communities (or consortia) and for understanding how natural systems may respond to changes in key environmental variables (e.g., climate change).

Microbial Mat Communities along an Oxygen Gradient in a Perennially Ice-Covered Antarctic Lake.

Lake Fryxell is a perennially ice-covered lake in the McMurdo Dry Valleys, Antarctica, with a sharp oxycline in a water column that is density stabilized by a gradient in salt concentration. Dissolved oxygen falls from 20 mg liter(-1) to undetectable over one vertical meter from 8.9- to 9.9-m depth. We provide the first description of the benthic mat community that falls within this oxygen gradient on the sloping floor of the lake, using a combination of micro- and macroscopic morphological descriptions, pigment analysis, and 16S rRNA gene bacterial community analysis. Our work focused on three macroscopic mat morphologies that were associated with different parts of the oxygen gradient: (i) "cuspate pinnacles" in the upper hyperoxic zone, which displayed complex topography and were dominated by phycoerythrin-rich cyanobacteria attributable to the genus Leptolyngbya and a diverse but sparse assemblage of pennate diatoms; (ii) a less topographically complex "ridge-pit" mat located immediately above the oxic-anoxic transition containing Leptolyngbya and an increasing abundance of diatoms; and (iii) flat prostrate mats in the upper anoxic zone, dominated by a green cyanobacterium phylogenetically identified as Phormidium pseudopriestleyi and a single diatom, Diadesmis contenta. Zonation of bacteria was by lake depth and by depth into individual mats. Deeper mats had higher abundances of bacteriochlorophylls and anoxygenic phototrophs, including Chlorobi and Chloroflexi. This suggests that microbial communities form assemblages specific to niche-like locations. Mat morphologies, underpinned by cyanobacterial and diatom composition, are the result of local habitat conditions likely defined by irradiance and oxygen and sulfide concentrations.

Distribution of cold adaptation proteins in microbial mats in Lake Joyce, Antarctica: Analysis of metagenomic data by using two bioinformatics tools

In this study, we report the distribution and abundance of cold-adaptation proteins in microbial mat communities in the perennially ice-covered Lake Joyce, located in the McMurdo Dry Valleys, Antarctica. We have used MG-RAST and R code bioinformatics tools on Illumina HiSeq2000 shotgun metagenomic data and compared the filtering efficacy of these two methods on cold-adaptation proteins. Overall, the abundance of cold-shock DEAD-box protein A (CSDA), antifreeze proteins (AFPs), fatty acid desaturase (FAD), trehalose synthase (TS), and cold-shock family of proteins (CSPs) were present in all mat samples at high, moderate, or low levels, whereas the ice nucleation protein (INP) was present only in the ice and bulbous mat samples at insignificant levels. Considering the near homogeneous temperature profile of Lake Joyce (0.08–0.29°C), the distribution and abundance of these proteins across various mat samples predictively correlated with known functional attributes necessary for microbial communities to thrive in this ecosystem. The comparison of the MG-RAST and the R code methods showed dissimilar occurrences of the cold-adaptation protein sequences, though with insignificant ANOSIM (R=0.357; p-value=0.012), ADONIS (R2=0.274; p-value=0.03) and STAMP (p-values=0.521–0.984) statistical analyses. Furthermore, filtering targeted sequences using the R code accounted for taxonomic groups by avoiding sequence redundancies, whereas the MG-RAST provided total counts resulting in a higher sequence output. The results from this study revealed for the first time the distribution of cold-adaptation proteins in six different types of microbial mats in Lake Joyce, while suggesting a simpler and more manageable user-defined method of R code, as compared to a web-based MG-RAST pipeline.

Functional Classification of Uncultured "Candidatus Caldiarchaeum subterraneum" Using the Maple System.

In this study, the metabolic and physiological potential evaluator system based on Kyoto Encyclopedia of Genes and Genomes (KEGG) functional modules was employed to establish a functional classification of archaeal species and to determine the comprehensive functions (functionome) of the previously uncultivated thermophile “Candidatus Caldiarchaeum subterraneum” (Ca. C. subterraneum). A phylogenetic analysis based on the concatenated sequences of proteins common among 142 archaea and 2 bacteria, and among 137 archaea and 13 unicellular eukaryotes suggested that Ca. C. subterraneum is closely related to thaumarchaeotic species. Consistent with the results of the phylogenetic analysis, clustering and principal component analyses based on the completion ratio patterns for all KEGG modules in 79 archaeal species suggested that the overall metabolic and physiological potential of Ca. C. subterraneum is similar to that of thaumarchaeotic species. However, Ca. C. subterraneum possessed almost no genes in the modules required for nitrification and the hydroxypropionate–hydroxybutyrate cycle for carbon fixation, unlike thaumarchaeotic species. However, it possessed all genes in the modules required for central carbohydrate metabolism, such as glycolysis, pyruvate oxidation, the tricarboxylic acid (TCA) cycle, and the glyoxylate cycle, as well as multiple sets of sugar and branched chain amino acid ABC transporters. These metabolic and physiological features appear to support the predominantly aerobic character of Ca. C. subterraneum, which lives in a subsurface thermophilic microbial mat community with a heterotrophic lifestyle.

Resilience and receptivity worked in tandem to sustain a geothermal mat community amidst erratic environmental conditions.

To elucidate how geothermal irregularities affect the sustainability of high-temperature microbiomes we studied the synecological dynamics of a geothermal microbial mat community (GMMC) vis-à-vis fluctuations in its environment. Spatiotemporally-discrete editions of a photosynthetic GMMC colonizing the travertine mound of a circum-neutral hot spring cluster served as the model-system. In 2010 a strong geyser atop the mound discharged mineral-rich hot water, which nourished a GMMC continuum from the proximal channels (PC) upto the slope environment (SE) along the mound’s western face. In 2011 that geyser extinguished and consequently the erstwhile mats disappeared. Nevertheless, two relatively-weaker vents erupted in the southern slope and their mineral-poor outflow supported a small GMMC patch in the SE. Comparative metagenomics showed that this mat was a relic of the 2010 community, conserved via population dispersal from erstwhile PC as well as SE niches. Subsequently in 2012, as hydrothermal activity augmented in the southern slope, ecological niches widened and the physiologically-heterogeneous components of the 2011 “seed-community” split into PC and SE meta-communities, thereby reclaiming either end of the thermal gradient. Resilience of incumbent populations, and the community’s receptiveness towards immigrants, were the key qualities that ensured the GMMC’s sustenance amidst habitat degradation and dispersal to discrete environments.

Quantitative PCR analysis of functional genes in iron-rich microbial mats at an active hydrothermal vent system (Lō'ihi Seamount, Hawai'i).

The chemolithotrophic Zetaproteobacteria represent a novel class of Proteobacteria which oxidize Fe(II) to Fe(III) and are the dominant bacterial population in iron-rich microbial mats. Zetaproteobacteria were first discovered at Lō'ihi Seamount, located 35 km southeast off the big island of Hawai'i, which is characterized by low-temperature diffuse hydrothermal venting. Novel nondegenerate quantitative PCR (qPCR) assays for genes associated with microbial nitrogen fixation, denitrification, arsenic detoxification, Calvin-Benson-Bassham (CBB), and reductive tricarboxylic acid (rTCA) cycles were developed using selected microbial mat community-derived metagenomes. Nitrogen fixation genes were not detected, but all other functional genes were present. This suggests that arsenic detoxification and denitrification processes are likely cooccurring in addition to two modes of carbon fixation. Two groups of microbial mat community types were identified by terminal restriction fragment length polymorphism (T-RFLP) and were further described based on qPCR data for zetaproteobacterial abundance and carbon fixation mode preference. qPCR variance was associated with mat morphology but not with temperature or sample site. Geochemistry data were significantly associated with sample site and mat morphology. Together, these qPCR assays constitute a functional gene signature for iron microbial mat communities across a broad array of temperatures, mat types, chemistries, and sampling sites at Lō'ihi Seamount.