Archaeal 16S rRNA Gene Sequences Research Articles

High diversity of planktonic prokaryotes in Arctic Kongsfjorden seawaters in summer 2015

Kongsfjorden is a typical glacier fjord in the European Arctic. In order to know the distribution and diversity of planktonic prokaryotes in the fjord subjected to strong physical gradient related with local glacier dynamics, prokaryote communities along a transect extending from the outer to the inner fjord was investigated in the summer of 2015 using 454 pyrosequencing of archaeal and bacterial 16S rRNA genes. Higher diversity and species richness were detected in Bacteria than in Archaea in each sample. Archaeal 16S rRNA gene sequences were not detected in the outer area of the fjord. Nitrososphaeria within the phylum Crenarchaeota and Poseidoniia within the Thermoplasmatota were two dominant archaeal groups in the fjord. At the genus level, Nitrosopumilus, Nitrosopelagicus, MGIIa-L1, and MGIIb–O2 dominated seawater archaeal communities. Higher abundances of Poseidoniale-related archaea were observed in the deep water than in the surface water. The Proteobacteria, Bacteroidota, and Actinobacteriota dominated the planktonic bacterial communities, with Verrucomicrobiota (represented by Verrucomicrobiae) dominating the middle area of the fjord. At the class level, Bacteroidia, Alphaproteobacteria, Gammaproteobacteria, and Actinobacteria dominated the bacterial communities within Kongsfjorden. Sequences affiliated with genera Polaribacter and Yoonia were frequently detected in the fjord. Results suggest that planktonic archaeal and bacterial community compositions in Kongsfjorden can be driven by different major environmental factors.

Intact Ether Lipids in Trench Sediments Related to Archaeal Community and Environmental Conditions in the Deepest Ocean

AbstractArchaea play an important role in marine biogeochemical cycle; however, their phylogenetic distribution and lipid composition in the hadal zone (6–11 km water depth) are poorly known. Here, we analyzed archaeal membrane lipids and 16S rRNA gene sequences in sediments from Mariana Trench (MT), Massau Trench (MS), and New Britain Trench (NBT), varying from 1,560 to 10,840 m depth. Forty‐two intact polar lipids (IPLs) were identified, including glycerol dialkyl glycerol tetraethers (GDGTs), OH‐GDGTs, glycerol dialkyl diethers (GDDs), and archaeol (AR) with polar headgroups of monohexose (1G), dihexose (2G), trihexose (3G), and hexose‐phosphohexose (HPH). Compositional and spatial distribution patterns of archaeal lipids suggest benthic Thaumarchaeota as a major source for IPLs, consistent with the predominance of Thaumarchaeota genes (>80%). The redundancy analysis (RDA) based on lipid and 16S rRNA data separates samples into three groups: extremely deep water (MT), significant terrestrial influence (NBT 1, 4, and 6), and predominant marine influence (MS, NBT 2, 3, 7, and 10). 1G‐GDDs and 1G‐AR positively correlate with water depth, likely reflecting the adaptation of benthic archaea to elevated hydrostatic pressure or variation of archaeal community in trench sediments. Bathyarchaeota are more abundant in sediments receiving terrestrial input; this pattern was attributed to their capability of utilizing terrestrial organic matter as an energy source. Our study highlights important environmental influences (e.g., pressure and organic matter quality and quantity) on benthic archaeal community and archaeal IPL compositions, which should be considered when IPLs and core lipids are applied as chemotaxonomic markers and paleo‐proxies.

Bacterial and archaeal communities in deep sea waters near the Ninetyeast Ridge in Indian Ocean

Depth-dependent distribution patterns of bacterial and archaeal communities in deep sea water column around the Ninetyeast Ridge in the Indian Ocean were investigated using 16S rRNA gene profiling. Sampling was conducted at the northern Ninetyeast Ridge (1°59.89′N–9°59.70′S, 87°58.90′E–88°00.03′E) from September to November 2016 where samples were collected from the bathyal (1 000 m) to bathypelagic depths (>4 000 m) in four different stations. A total of 1 565 405 clean data falling into 6 712 bacterial OTUs and 1 452 727 clean data falling into 806 archaeal OTUs based on 97% similarity level were analyzed. Most of the bacterial 16S rRNA gene sequences were affiliated with Gammaproteobacteria, followed by Alphaproteobacteria and Bacteroidia. The archaeal 16S rRNA gene sequences mostly affiliated to Nitrososphaeria (Thaumarchaeota) dominated with relative abundances ranging from 52.68% to 97.2%, followed by Thermoplasmata (Euryarchaeota). Vertical partitioning of bacterial and archaeal communities among different water layers was observed. Canonical correspondence analysis (CCA) and Spearman’s correlations revealed that depth (P=0.003), dissolved oxygen (P=0.019), and nitrite (P=0.033) were the main environmental factors affecting bacterial community structure at genus level in the Ninetyeast Ridge. On the other hand, the first two CCA axes accounted for 74.4% of the explained total variance, it seems that the archaeal communities at genus level were heavily influenced by the environmental variables including depth, dissolved oxygen (DO), nitrite, salinity, phosphate, ammonia, nitrate, and silicate, but none of them exhibited any significant correlation on the structuring (P>0.1).

Fluid inclusions from the deep Dead Sea sediment provide new insights on Holocene extreme microbial life

The Dead Sea Deep Drilling Project allowed us to retrieve a continuous sedimentary record spanning the two last glacial cycles. This unique archive, in such an extreme environment, has permitted the development of new proxies and the refinement of already available paleoenvironmental studies. Although life is pushed to its extremes in the Dead Sea environment, several studies have highlighted the impact of microbial activity on this harsh milieu. The identity and means of adaptation of these organisms are however partly ignored. We also know relatively little on the way this extreme ecosystem has evolved with time, and how it will react to growing pressure. In this study, we have used the fluid inclusions trapped in halite, the main evaporitic phase during arid periods in the Dead Sea, to investigate the way the Dead Sea ecosystem has evolved. By extracting ancient DNA from Holocene halite fluid inclusions, we have obtained fossil bacterial and archaeal 16S rRNA gene sequences that suggest that the main microbial actors of the present Dead Sea have been present in the lake for a relatively long period, emphasizing the stability of this extreme environment. This is the case of extreme halophilic archaea of the Salinarchaeum genera. Additionally, we show that current phylotypes of the deep biosphere, such as Acetothermia bacteria are present within the obtained fluid inclusions sequences, which would support seeding of the deep biosphere from the water column. Finally, through the retrieval of sequences assigned to Halodesulfurarchaeum and Desulfovermiculus genera, we shed light on putative new actors of the sulfur cycle involving respectively archaea and bacteria, which could play an unexpected role in the reduction of sulfur species. Together, these data provide new research avenues for both geologists and biologists working in this extreme environment, and help to increase understanding of the evolution of the Dead Sea ecosystem with time.

Phylogenetic characterization of eukaryotic and prokaryotic gut flora of Nile tilapia, Oreochromis niloticus, along niches of Lake Nasser, Egypt, based on rRNA gene high-throughput sequences

Abstract Studies of phylogenetic diversity of fish gut flora often focus on bacteria, leaving a gap in characterization of flora from other domains. This study focused on first exploring of phylogenetic composition of the gut flora, belonging to all domains, eukaryotes, bacteria and archaea, of the tilapia fish, Oreochromis niloticus, inhabiting Lake Nasser, Egypt, based on rRNA gene high-throughput sequencing. Specimens were collected from four distant lake natural fish feeding niches, Khor Kalabsha, Khor Wadi Abyad, Khor Korosko and Khor Toshka. Metagenomic DNA was extracted from fish gut contents, followed by PCR and next generation sequencing of both of eukaryotic 18S- and prokaryotic 16S rRNA genes. A total of 2491, 19005 and 9032 rRNA gene OTUs, were recorded, for eukaryotes, bacteria and archaea, respectively, in the guts from the four niches. Fish guts from Khor Toshka, harbored the highest diversity of bacterial and archaeal 16S rRNA gene sequences. Some 18S rRNA gene OTUs, belonging to members of class Ostracoda, molluscs, and phylum Bacillariophyta, diatoms, beside of 16S rRNA gene OTUs assigned to genus Synechococcus, phylum Cyanobacteria, were recorded in guts from all studied niches, suggesting favorite foods for the fish throughout the lake. Other rRNA gene OTUs, affiliated with the diatom genus Fragilaria, cyanobacterial family Pseudanabaenaceae and genus Oscillatoria, characterized guts from Khor Toshka and Khor Kalabsha, respectively. OTUs, belonging to genus Cetobacterium, phylum Fusobacteria; genera, Methanobacterium and Methanosaeta, phylum Euryarchaeota, constituted the core gut microbiome. Neoechinorhynchus-like OTUs were recorded in guts from all niches, implicating common tilapia gut parasites at Lake Nasser. Guts from all niches harbored several unique archaeal 16S rRNA gene OTUs, but did not match known archaeal phyla. Hence, a large number of phylogenetic shared taxa persist across guts from distant niches, with respect to some OTUs, characterizing gut contents of specific niches.

Petroleum hydrocarbon rich oil refinery sludge of North-East India harbours anaerobic, fermentative, sulfate-reducing, syntrophic and methanogenic microbial populations

BackgroundSustainable management of voluminous and hazardous oily sludge produced by petroleum refineries remains a challenging problem worldwide. Characterization of microbial communities of petroleum contaminated sites has been considered as the essential prerequisite for implementation of suitable bioremediation strategies. Three petroleum refinery sludge samples from North Eastern India were analyzed using next-generation sequencing technology to explore the diversity and functional potential of inhabitant microorganisms and scope for their on-site bioremediation.ResultsAll sludge samples were hydrocarbon rich, anaerobic and reduced with sulfate as major anion and several heavy metals. High throughput sequencing of V3-16S rRNA genes from sludge metagenomes revealed dominance of strictly anaerobic, fermentative, thermophilic, sulfate-reducing bacteria affiliated to Coprothermobacter, Fervidobacterium, Treponema, Syntrophus, Thermodesulfovibrio, Anaerolinea, Syntrophobacter, Anaerostipes, Anaerobaculum, etc., which have been well known for hydrocarbon degradation. Relatively higher proportions of archaea were detected by qPCR. Archaeal 16S rRNA gene sequences showed presence of methanogenic Methanobacterium, Methanosaeta, Thermoplasmatales, etc. Detection of known hydrocarbon utilizing aerobic/facultative anaerobic (Mycobacterium, Pseudomonas, Longilinea, Geobacter, etc.), nitrate reducing (Gordonia, Novosphigobium, etc.) and nitrogen fixing (Azovibrio, Rhodobacter, etc.) bacteria suggested niche specific guilds with aerobic, facultative anaerobic and strict anaerobic populations. Phylogenetic Investigation of Communities by Reconstruction of Unobserved States (PICRUSt) predicted putative genetic repertoire of sludge microbiomes and their potential for hydrocarbon degradation; lipid-, nitrogen-, sulfur- and methane- metabolism. Methyl coenzyme M reductase A (mcrA) and dissimilatory sulfite reductase beta-subunit (dsrB) genes phylogeny confirmed methanogenic and sulfate-reducing activities within sludge environment endowed by hydrogenotrophic methanogens and sulfate-reducing Deltaproteobacteria and Firmicutes members.ConclusionRefinery sludge microbiomes were comprised of hydrocarbon degrading, fermentative, sulfate-reducing, syntrophic, nitrogen fixing and methanogenic microorganisms, which were in accordance with the prevailing physicochemical nature of the samples. Analysis of functional biomarker genes ascertained the activities of methanogenic and sulfate-reducing organisms within sludge environment. Overall data provided better insights on microbial diversity and activity in oil contaminated environment, which could be exploited suitably for in situ bioremediation of refinery sludge.

Diversity and distribution of Archaea in global estuarine ecosystems

Estuarine ecosystem is a unique geographical transitional zone between freshwater and seawater, harboring a wide range of microbial communities including Archaea. Although a large number of Archaea have been detected in such ecosystem, the global patterns in archaeal diversity and distribution are extremely scarce. To bridge this gap, we carried out a comprehensive survey of archaeal communities using ca. 4000 publicly available archaeal 16S rRNA gene sequences (>300 bp) collected from 24 estuaries in different latitude regions. These sequences were divided into 1450 operational taxonomic units (OTUs) at 97% identity, suggesting a high biodiversity that increased gradually from the high- to low-latitude estuaries. Phylogenetic analysis showed that estuarine ecosystem was a large biodiversity pool of Archaea that was mainly composed of 12 phyla. Among them, the predominant groups were Bathyarchaeota, Euryarchaeota and Thaumarchaeota. Interestingly, archaeal distribution demonstrated a geographical differentiation in that Thaumarchaeota was dominated in the low-latitude estuaries, Bathyarchaeota in the mid-latitude estuaries, and Euryarchaeota in the high-latitude estuaries, respectively. Furthermore, the majority of the most abundant 20 OTUs demonstrated an overrepresented or underrepresented distribution pattern in some specific estuaries or latitude regions while a few were evenly distributed throughout the estuaries. This pattern indicates a potential selectivity of geographical distribution. In addition, the analysis of environmental parameters suggested that latitude would be one of the major factors driving the distribution of archaeal communities in estuarine ecosystem. This study profiles a clear framework on the diversity and distribution of Archaea in the global estuarine ecosystem and explores the general environmental factors that influence these patterns. Our findings constitute an important part of the exploration of the global ecology of Archaea.

Archaea are prominent members of the prokaryotic communities colonizing common forest mushrooms.

In this study, the abundance and composition of prokaryotic communities associated with the inner tissue of fruiting bodies of Suillus bovinus, Boletus pinophilus, Cantharellus cibarius, Agaricus arvensis, Lycoperdon perlatum, and Piptoporus betulinus were analyzed using culture-independent methods. Our findings indicate that archaea and bacteria colonize the internal tissues of all investigated specimens and that archaea are prominent members of the prokaryotic community. The ratio of archaeal 16S rRNA gene copy numbers to those of bacteria was >1 in the fruiting bodies of four out of six fungal species included in the study. The largest proportion of archaeal 16S rRNA gene sequences belonged to thaumarchaeotal classes Terrestrial group, Miscellaneous Crenarchaeotic Group (MCG), and Thermoplasmata. Bacterial communities showed characteristic compositions in each fungal species. Bacterial classes Gammaproteobacteria, Actinobacteria, Bacilli, and Clostridia were prominent among communities in fruiting body tissues. Bacterial populations in each fungal species had different characteristics. The results of this study imply that fruiting body tissues are an important habitat for abundant and diverse populations of archaea and bacteria.

Molecular analysis of methanogen populations and their interactions within anaerobic sludge digesters

ABSTRACTKnowledge of archaeal population structure, function and interactions is of great interest for a deeper understanding of the anaerobic digestion step in wastewater treatment process, that represents a bottle neck in the optimization of digesters performance. Although culture-independent techniques have enabled the exploration of archaeal population in such systems, their population dynamics and interactions still require further investigation. In the present study, 2646 almost full archaeal 16S rRNA gene sequences retrieved from 22 anaerobic digesters located worldwide were analyzed and classified into 83 Operational Taxonomic Units (OTUs) for Euryarchaeotes and 2 OTUs for Crenarchaeotes. Among the Euryarchaeotes, Methanosarcinales represent the predominant archaeal population (47.5% of total sequences), followed by the ARC I (WSA2) lineage (25.3%), Methanomicrobiales (19.9%) and Methanobacteriales (1.9%). Theses lineages are predominant in nine, five, two and one digesters respectively. However, the remaining 5 digesters show no predominance of any methanogenic group. According to the predominance of theses lineages, 5 digester profiles were distinguished. This study revealed a clear interaction between the 4 methanogenic lineages. A core of 12 OTUs represented by five, four, two and one OTU for Methanosarcinales, Methanomicrobiales, ARC I and Methanobacteriales respectively were quantitatively abundant in at least 50% of the analyzed digesters. 16S rRNA targeted hybridization oligonucleotide probes targeting the predominant OTUs are being developed to follow their population dynamics under various parameters.

Seasonal and depth-wise variations in bacterial and archaeal groups in the Arabian Sea oxygen minimum zone

Seasonal variations, as well as depth-wise distribution patterns of bacterial and archaeal communities in the Arabian Sea oxygen minimum zone (AS-OMZ), were analyzed by examining 16S rRNA gene clones and their sequences. Sampling was carried out at the Arabian Sea Time Series (ASTS) location (17°0.126′ N, 67°59.772′ E) from five different depths during three different seasons. A total of 743 and 256 non-chimeric bacterial and archaeal 16S rRNA gene sequences were analyzed. Most of the bacterial 16S rRNA gene sequences were affiliated to Gammaproteobacteria (39.31%), Alphaproteobacteria (23.56%) and Cyanobacteria (20.2%). The archaeal 16S rRNA gene sequences mostly aligned with Marine Group II (MG-II, Euryarchaeota). An explicit vertical partitioning of bacterial communities between the surface (surface and DCM) and OMZ (250 m, 500 m, and 1000 m) was observed. Also evident was an apparent seasonal variation among surface bacterial communities but a minimal variation among OMZ bacterial and archaeal communities. LINKTREE and canonical correspondence analysis (CCA) indicates that differences in the concentrations of dissolved oxygen (DO) and total organic carbon (TOC) seem to cause the vertical separation among bacterial communities in the ASTS station. A higher number of shared OTUs affiliated mainly to Alteromonadales (bacteria) and Methanosarcinales (archaea) contributed towards seasonally stable community structure in the OMZ depths.

Links between seawater flooding, soil ammonia oxidiser communities and their response to changes in salinity.

Coastal areas worldwide are challenged by climate change-associated increases in sea level and storm surge quantities that potentially lead to more frequent flooding of soil ecosystems. Currently, little is known of the effects of inundation events on microorganisms controlling nitrification in these ecosystems. The goal of this study was to investigate the impact of seawater flooding on the abundance, community composition and salinity tolerance of soil ammonia oxidisers. Topsoil was sampled from three islands flooded at different frequencies by the Wadden Sea. Archaeal ammonia oxidiser amoA genes were more abundant than their betaproteobacterial counterparts, and the distribution of archaeal and bacterial ammonia oxidiser amoA and 16S rRNA gene sequences significantly differed between the islands. The findings indicate selection of ammonia oxidiser phylotypes with greater tolerance to high salinity and slightly alkaline pH (e.g. Nitrosopumilus representatives) in frequently flooded soils. A cluster phylogenetically related to gammaproteobacterial ammonia oxidisers was detected in all samples analysed in this survey. Nevertheless, no gammaprotebacterial amoA genes could be amplified via PCR and only betaproteobacterial ammonia oxidisers were detected in enrichment cultures. A slurry-based experiment demonstrated the tolerance of both bacterial and archaeal ammonia oxidisers to a wide range of salinities (e.g. Wadden Sea water salinity) in soil naturally exposed to seawater at a high frequency.

Methane emission from feather moss stands.

Data from remote sensing and Eddy towers indicate that forests are not always net sinks for atmospheric CH4 . However, studies describing specific sources within forests and functional analysis of microorganisms on sites with CH4 turnover are scarce. Feather moss stands were considered to be net sinks for carbon dioxide, but received little attention to their role in CH4 cycling. Therefore, we investigated methanogenic rates and pathways together with the methanogenic microbial community composition in feather moss stands from temperate and boreal forests. Potential rates of CH4 emission from intact moss stands (n = 60) under aerobic conditions ranged between 19 and 133 pmol CH4 h-1 gdw-1 . Temperature and water content positively influenced CH4 emission. Methanogenic potentials determined under N2 atmosphere in darkness ranged between 22 and 157 pmol CH4 h-1 gdw-1 . Methane production was strongly inhibited by bromoethane sulfonate or chloroform, showing that CH4 was of microbial origin. The moss samples tested contained fluorescent microbial cells and between 104 and 105 copies per gram dry weight moss of the mcrA gene coding for a subunit of the methyl CoM reductase. Archaeal 16S rRNA and mcrA gene sequences in the moss stands were characteristic for the archaeal families Methanobacteriaceae and Methanosarcinaceae. The potential methanogenic rates were similar in incubations with and without methyl fluoride, indicating that the CH4 was produced by the hydrogenotrophic rather than aceticlastic pathway. Consistently, the CH4 produced was depleted in 13 C in comparison with the moss biomass carbon and acetate accumulated to rather high concentrations (3-62 mM). The δ13 C of acetate was similar to that of the moss biomass, indicating acetate production by fermentation. Our study showed that the feather moss stands contained active methanogenic microbial communities producing CH4 by hydrogenotrophic methanogenesis and causing net emission of CH4 under ambient conditions, albeit at low rates.

Diversity of Archaea in Bottom Sediments of the Discharge Areas With Oil- and Gas-Bearing Fluids in Lake Baikal

ABSTRACTUsing massively parallel sequencing (the Roche 454 platform) we have studied the diversity of archaeal 16S rRNA gene sequences in oxic and anoxic sediments at six sites in Lake Baikal with oil- and gas-bearing fluids discharge. Archaeal communities appeared to be represented mainly by five phyla: Euryarchaeota, Crenarchaeota, Thaumarchaeota, Bathyarchaeota (miscellaneous Crenarchaeotic group), and Woesearchaeota (deep sea hydrothermal vent group 6). Among them we detected sequences of methanogens of the orders Methanomicrobiales, Methanosarsinales, Methanococcales, as well as representatives of the following uncultured archaeal lineages: Group C3, Marine Benthic Group D, and Terrestrial Miscellaneous Group. We have also identified sequences of ammonia-oxidizing archaea of the phyla Crenarchaeota and Thaumarchaeota. Phylogenetic analysis showed the presence ANME-2d-related sequences. However, the analysis of mcrA genes libraries has not revealed typical representatives of ANME groups. Comparison of amplicon libraries 16S rRNA gene fragments from different samples proved the widespread presence of previously detected Baikal archaeal lineages, which are members of the phylum Crenarchaeota and Thaumarchaeota (formerly Group C3 of Crenarchaeota).

Microbial Community Ability to Adapt to Altered Temperature Conditions Influences Operating Stability in Anaerobic Digestion

Abstract This study examined the influence of altered operating temperature on microbial community composition and how this affects the ability of anaerobic degradation (AD) processes to cope with increasing loading rate. Four digesters fed household and slaughterhouse waste, mimicking two large-scale processes, were operated in sets of two at 37°C or 52°C, followed by a gradual increase or decrease in temperature in one digester in each set. All digesters were then subjected to step-wise increases in organic loading rate (OLR) from 3 to 7g VS/L/day, concurrently with decreased hydraulic retention time (HRT). Temporal microbial changes were monitored by Illumina MiSeq analysis of bacterial and archaeal 16S rRNA gene sequences. The digester transformed from thermophilic to mesophilic conditions failed at 6g VS/L/day, whereas the reference digesters and the mesophilic-to-thermophilic digester remained stable at all OLR investigated. The bacterial community was characterised by relatively diversified structure dominated by Bacteriodetes and Firmicutes in mesophilic conditions. Increasing temperature caused loss of complexity at phyla level and enhanced the relative abundance of Firmicutes and Thermotogae. Temperature adaptation in the thermophilic-to-mesophilic digester resulted in a bacterial community structure reflecting the communities observed in digesters with initial temperature of 37°C. However, certain populations found in the mesophilic digesters did not appear at detectable levels during operation at 37°C in the thermophilic-to-mesophilic digester. Overall, the results showed that anaerobic process stability was highly dependent on the innate resilience of the microbial community. The mesophilic microbiota formed from a thermophilic community had a slightly different structure than its mesophilic counterpart and was considerably less resistant to increased OLR in digesters examined within this study.

Biomarkers and Metabolic Patterns in the Sediments of Evolving Glacial Lakes as a Proxy for Planetary Lake Exploration.

Oligotrophic glacial lakes in the Andes Mountains serve as models to study the effects of climate change on natural biological systems. The persistent high UV regime and evolution of the lake biota due to deglaciation make Andean lake ecosystems potential analogues in the search for life on other planetary bodies. Our objective was to identify microbial biomarkers and metabolic patterns that represent time points in the evolutionary history of Andean glacial lakes, as these may be used in long-term studies as microscale indicators of climate change processes. We investigated a variety of microbial markers in shallow sediments from Laguna Negra and Lo Encañado lakes (Región Metropolitana, Chile). An on-site immunoassay-based Life Detector Chip (LDChip) revealed the presence of sulfate-reducing bacteria, methanogenic archaea, and exopolymeric substances from Gammaproteobacteria. Bacterial and archaeal 16S rRNA gene sequences obtained from field samples confirmed the results from the immunoassays and also revealed the presence of Alpha-, Beta-, Gamma-, and Deltaproteobacteria, as well as cyanobacteria and methanogenic archaea. The complementary immunoassay and phylogenetic results indicate a rich microbial diversity with active sulfate reduction and methanogenic activities along the shoreline and in shallow sediments. Sulfate inputs from the surrounding volcanic terrains during deglaciation may explain the observed microbial biomarker and metabolic patterns, which differ with depth and between the two lakes. A switch from aerobic and heterotrophic metabolisms to anaerobic ones such as sulfate reduction and methanogenesis in the shallow shores likely reflects the natural evolution of the lake sediments due to deglaciation. Hydrodynamic deposition of sediments creates compartmentalization (e.g., sediments with different structure and composition surrounded by oligotrophic water) that favors metabolic transitions. Similar phenomena would be expected to occur on other planetary lakes, such as those of Titan, where watery niches fed by depositional events would be surrounded by a "sea" of hydrocarbons. Key Words: Glacier lakes-Sedimentation-Prokaryotic metabolisms and biomarkers-Deglaciation-Life detection-Planetary exploration. Astrobiology 18, 586-606.

Dense microbial community on a ferromanganese nodule from the ultra-oligotrophic South Pacific Gyre: Implications for biogeochemical cycles

Abstract During Integrated Ocean Drilling Program (IODP) Expedition 329, a deep-sea ferromanganese nodule and surrounding sediment were collected from the South Pacific Gyre, the most oligotrophic oceanic environment on earth. Using a combination of cryo-sectioning and fluorescence-based cell counting techniques, we determined that the microbial cell density at the very surface of the nodule was ∼108 cells cm−3, three orders of magnitude higher than that in the surrounding sediment. Analysis of bacterial and archaeal 16S rRNA gene sequences (∼1400 bp) indicated that the taxonomic composition of the nodule-associated community differed markedly from that of the sediment-associated community. Members of Marine Group I (MGI) Thaumarchaeota are potentially crucial for sustaining the high cell density because both ammonia and Cu were available on the nodule surface, making it suitable for ammonia-oxidizing chemolithoautotrophy mediated by copper enzymes. Combined cryo-sectioning and synchrotron analysis of the nodule surface revealed both hexagonal birnessite resembling δ-MnO2 and triclinic birnessite, minerals characteristic of biogenic oxide and its secondary product, respectively. Regardless of these possible biogenic features, only one gene sequence exhibited some similarity to previously identified manganese-oxidizing bacteria. On the other hand, MGI Thaumarchaeota were assumed as potential candidate of manganese oxidizers because they have multi-copper oxidase that is utilized by most known manganese oxidizers. Therefore, this archaeal group is considered to play a significant ecological role as a primary producer in biogeochemical elemental cycles in the ultra-oligotrophic abyssal plain.

Biological Phosphorus Removal During High-Rate, Low-Temperature, Anaerobic Digestion of Wastewater.

We report, for the first time, extensive biologically mediated phosphate removal from wastewater during high-rate anaerobic digestion (AD). A hybrid sludge bed/fixed-film (packed pumice stone) reactor was employed for low-temperature (12°C) anaerobic treatment of synthetic sewage wastewater. Successful phosphate removal from the wastewater (up to 78% of influent phosphate) was observed, mediated by biofilms in the reactor. Scanning electron microscopy and energy dispersive X-ray analysis revealed the accumulation of elemental phosphorus (∼2%) within the sludge bed and fixed-film biofilms. 4′, 6-diamidino-2-phenylindole (DAPI) staining indicated phosphorus accumulation was biological in nature and mediated through the formation of intracellular inorganic polyphosphate (polyP) granules within these biofilms. DAPI staining further indicated that polyP accumulation was rarely associated with free cells. Efficient and consistent chemical oxygen demand (COD) removal was recorded, throughout the 732-day trial, at applied organic loading rates between 0.4 and 1.5 kg COD m-3 d-1 and hydraulic retention times of 8–24 h, while phosphate removal efficiency ranged from 28 to 78% on average per phase. Analysis of protein hydrolysis kinetics and the methanogenic activity profiles of the biomass revealed the development, at 12°C, of active hydrolytic and methanogenic populations. Temporal microbial changes were monitored using Illumina MiSeq analysis of bacterial and archaeal 16S rRNA gene sequences. The dominant bacterial phyla present in the biomass at the conclusion of the trial were the Proteobacteria and Firmicutes and the dominant archaeal genus was Methanosaeta. Trichococcus and Flavobacterium populations, previously associated with low temperature protein degradation, developed in the reactor biomass. The presence of previously characterized polyphosphate accumulating organisms (PAOs) such as Rhodocyclus, Chromatiales, Actinobacter, and Acinetobacter was recorded at low numbers. However, it is unknown as yet if these were responsible for the luxury polyP uptake observed in this system. The possibility of efficient phosphate removal and recovery from wastewater during AD would represent a major advance in the scope for widespread application of anaerobic wastewater treatment technologies.

Distinctive non-methanogen archaeal populations in anaerobic digestion.

Methanogens define the archaeal communities involved in anaerobic digestion. Recently, non-methanogen archaeal populations have been unexpectedly identified in anaerobic digestion processes. To gain insight into the ecophysiology of these uncharacterized archaeal populations, for the first time, a phylogenetic analysis was performed on a collection of non-methanogen archaeal 16S rRNA gene sequences from anaerobic digesters of broad geographic distribution, revealing a distinct clade formed by these sequences in subgroup 6 of the Miscellaneous Crenarchaeotal Group in the newly proposed archaeal phylum Bathyarchaeota. This exclusive phylogenetic assemblage enabled the development of a real-time quantitative PCR (qPCR) assay specifically targeting these non-methanogen archaeal populations in anaerobic digestion. Application of the qPCR assay in continuous anaerobic digesters indicated that these archaeal populations were minor constituents of the archaeal communities, and the abundance of these populations remained relatively constant irrespective of process perturbations. Analysis of the archaeal populations in methanogenic communities further revealed the co-occurrence of these non-methanogen archaea with acetoclastic methanogens. Nevertheless, the low abundance of non-methanogen archaea as compared with acetoclastic methanogens suggests that the non-methanogen archaeal populations were not major players in animal waste-fed methanogenic processes investigated in this study and the functions of these archaeal populations remain to be identified.

Methane-related changes in prokaryotes along geochemical profiles in sediments of Lake Kinneret (Israel)

Abstract. Microbial methane oxidation is the primary control on the emission of the greenhouse gas methane into the atmosphere. In terrestrial environments, aerobic methanotrophic bacteria are largely responsible for this process. In marine sediments, a coupling of anaerobic oxidation of methane (AOM) with sulfate reduction, often carried out by a consortium of anaerobic methanotrophic archaea (ANME) and sulfate-reducing bacteria, consumes almost all methane produced within those sediments. Motivated by recent evidence for AOM with iron(III) in Lake Kinneret sediments, the goal of the present study was to link the geochemical gradients in the lake porewater to the microbial community structure. Screening of archaeal 16S rRNA gene sequences revealed a shift from hydrogenotrophic to acetoclastic methanogens with depth. The observed changes in microbial community structure suggest possible direct and indirect mechanisms for the AOM coupled to iron reduction in deep sediments. The percentage of members of the Nitrospirales order increased with depth, suggesting their involvement in iron reduction together with Geobacter genus and "reverse methanogenesis". An indirect mechanism through sulfate and ANME seems less probable due to the absence of ANME sequences. This is despite the abundant sequences related to sulfate-reducing bacteria (Deltaproteobacteria) together with the occurrence of dsrA in the deep sediment that could indicate the production of sulfate (disproportionation) from S0 for sulfate-driven AOM. The presence of the functional gene pmoA in the deep anoxic sediment together with sequences related to Methylococcales suggests the existence of a second unexpected indirect pathway – aerobic methane oxidation pathway in an anaerobic environment.

The Archaea Community Associated with Lava-Formed Gotjawal Forest Soil in Jeju, Korea

The abundance and diversity of archaeal assemblages were analyzed in soils collected from Gyorae Gotjawal forest, Jeju, Korea. Gotjawal soil refers to soil derived from a lava-formed forest, characterized by high organic matter content, fertility, and poor rocky soil. Using domain-specific primers, archaeal 16S rRNA gene sequences were PCR amplified for clone library construction, and a total of 185 archaeal clones were examined. The archaeal clones were affiliated with the phyla Thaumarchaeota (96.2%) and Euryarchaeota (3.8%). The most abundant thaumarchaeal group (90.3% of the clones) was the group I.1b clade, which includes soil ammonia-oxidizing archaea. The unique characteristics of Gotjawal soil, including basalt morphology, vegetation, and groundwater aquifer penetration, may be reflected in the archaeal community composition. Further study is necessary to understand the unique factors of Gotjawal soils that influence archaeal abundance, composition, and diversity.