Phylogenetic diversity of bacterial and archaeal communities in the anoxic zone of the Cariaco Basin

First report of betalain production from endolichenic Bacillus sp. LDAB-1 from Dirinaria aegilita: Insights from novel quantification methodology of image processing

Pigments are widely used in food supplements envisaging attractive colors along with health benefits. The desired advancements in the nutraceutical and antioxidant properties of pigments utilized in food products necessitate the search for novel additives. The present study is the first in the field to report the pigment-producing endolichenic bacteria, Bacillus sp. LDAB-1 from Dirinaria aegilita. Morphological, biochemical, and molecular characterization of the bacterium emphasizes that ideal pigment production occurs when utilizing sucrose and sodium nitrate. The pigment was salted out and dialyzed for further qualitative characterization using ultraviolet-visible, fluorescence, and Fourier transform infrared spectra and the results corroborated the presence of betalains. The antioxidant activity of betalain is closer to the efficiency of α-tocopherol, which confers the pigment properties for antioxidant and nutraceutical significance. An optimal methodology for pigment affirmation is an issue when using an alternative methodology. Hence, the present assessment employs a comparative analysis of findings from both a spectrophotometric method and image processing technology encompassing RGB, CMYK, YCbCr, and L*a*b* color space models. Amongst these, the L*a*b* model potentially provides an effective modality for determining the pigment concentration. Bland-Altman plot analysis indicates similar consistency levels in betalain quantification by both methods at 95% confidence intervals, affirming the integrity and consistency of color image processing technology. Consequently, the present study represents novelty and innovativeness in reporting endolichenic Bacillus sp. LDAB-1 from D. aegilita and a rational image optimization protocol for pigment elucidation characteristics.

Autotrophic biofilms sustained by deeply sourced groundwater host diverse bacteria implicated in sulfur and hydrogen metabolism

BACKGROUND

Biofilms in sulfide-rich springs present intricate microbial communities that play pivotal roles in biogeochemical cycling. We studied chemoautotrophically based biofilms that host diverse CPR bacteria and grow in sulfide-rich springs to investigate microbial controls on biogeochemical cycling.

RESULTS

Sulfide springs biofilms were investigated using bulk geochemical analysis, genome-resolved metagenomics, and scanning transmission X-ray microscopy (STXM) at room temperature and 87 K. Chemolithotrophic sulfur-oxidizing bacteria, including Thiothrix and Beggiatoa, dominate the biofilms, which also contain CPR Gracilibacteria, Absconditabacteria, Saccharibacteria, Peregrinibacteria, Berkelbacteria, Microgenomates, and Parcubacteria. STXM imaging revealed ultra-small cells near the surfaces of filamentous bacteria that may be CPR bacterial episymbionts. STXM and NEXAFS spectroscopy at carbon K and sulfur L2,3 edges show that filamentous bacteria contain protein-encapsulated spherical elemental sulfur granules, indicating that they are sulfur oxidizers, likely Thiothrix. Berkelbacteria and Moranbacteria in the same biofilm sample are predicted to have a novel electron bifurcating group 3b [NiFe]-hydrogenase, putatively a sulfhydrogenase, potentially linked to sulfur metabolism via redox cofactors. This complex could potentially contribute to symbioses, for example, with sulfur-oxidizing bacteria such as Thiothrix that is based on cryptic sulfur cycling. One Doudnabacteria genome encodes adjacent sulfur dioxygenase and rhodanese genes that may convert thiosulfate to sulfite. We find similar conserved genomic architecture associated with CPR bacteria from other sulfur-rich subsurface ecosystems.

CONCLUSIONS

Our combined metagenomic, geochemical, spectromicroscopic, and structural bioinformatics analyses of biofilms growing in sulfide-rich springs revealed consortia that contain CPR bacteria and sulfur-oxidizing Proteobacteria, including Thiothrix, and bacteria from a new family within Beggiatoales. We infer roles for CPR bacteria in sulfur and hydrogen cycling. Video Abstract.

K. Habeebullah S, Ali AK, Al-Zakri WM. Diversity and spatiotemporal variations in bacterial and archaeal communities within Kuwaiti territorial waters of the Northwest Arabian Gulf

Kuwaiti territorial waters of the northwest Arabian Gulf represent a unique aquatic ecosystem prone to various environmental and anthropogenic stressors that pose significant constraints on the resident biota which must withstand extreme temperatures, salinity levels, and reducing conditions, among other factors to survive. Such conditions create the ideal environment for investigations into novel functional genetic adaptations of resident organisms. Firstly, however, it is essential to identify said organisms and understand the dynamic nature of their existence. Thus, this study provides the first comprehensive analysis of bacterial and archaeal community structures in the unique waters of Kuwait located in the Northwest Arabian Gulf and analyzes their variations with respect to depth, season, and location, as well as their susceptibility to changes in abundance with respect to various physicochemical parameters. Importantly, this study is the first of its kind to utilize a shotgun metagenomics approach with sequencing performed at an average depth of 15 million paired end reads per sample, which allows for species-level community profiling and sets the framework for future functional genomic investigations. Results showed an approximately even abundance of both archaeal (42.9%) and bacterial (57.1%) communities, but significantly greater diversity among the bacterial population, which predominantly consisted of members of the Proteobacteria, Cyanobacteria, and Bacteroidetes phyla in decreasing order of abundance. Little to no significant variations as assessed by various metrics including alpha and beta diversity analyses were observed in the abundance of archaeal and bacterial populations with respect to depth down the water column. Furthermore, although variations in differential abundance of key genera were detected at each of the three sampling locations, measurements of species richness and evenness revealed negligible variation (ANOVA p<0.05) and only a moderately defined community structure (ANOSIM r2 = 0.243; p>0.001) between the various locations. Interestingly, abundance of archaeal community members showed a significant increase (log2 median ratio of RA = 2.6) while the bacterial population showed a significant decrease (log2 median ratio = -1.29) in the winter season. These findings were supported by alpha and beta diversity analyses as well (ANOSIM r2 = 0.253; p>0.01). Overall, this study provides the first in-depth analysis of both bacterial and archaeal community structures developed using a shotgun metagenomic approach in the waters of the Northwest Arabian Gulf thus providing a framework for future investigations of functional genetic adaptations developed by resident biota attempting to survive in the uniquely extreme conditions to which they are exposed.

Eukaryotic Parasites Are Integral to a Productive Microbial Food Web in Oxygen-Depleted Waters

Oxygen-depleted water columns (ODWCs) host a diverse community of eukaryotic protists that change dramatically in composition over the oxic-anoxic gradient. In the permanently anoxic Cariaco Basin, peaks in eukaryotic diversity occurred in layers where dark microbial activity (chemoautotrophy and heterotrophy) were highest, suggesting a link between prokaryotic activity and trophic associations with protists. Using 18S rRNA gene sequencing, parasites and especially the obligate parasitic clade, Syndiniales, appear to be particularly abundant, suggesting parasitism is an important, but overlooked interaction in ODWC food webs. Syndiniales were also associated with certain prokaryotic groups that are often found in ODWCs, including Marinimicrobia and Marine Group II archaea, evocative of feedbacks between parasitic infection events, release of organic matter, and prokaryotic assimilative activity. In a network analysis that included all three domains of life, bacterial and archaeal taxa were putative bottleneck and hub species, while a large proportion of edges were connected to eukaryotic nodes. Inclusion of parasites resulted in a more complex network with longer path lengths between members. Together, these results suggest that protists, and especially protistan parasites, play an important role in maintaining microbial food web complexity, particularly in ODWCs, where protist diversity and microbial productivity are high, but energy resources are limited relative to euphotic waters.

Microbial Ecology of Oxygen Minimum Zones Amidst Ocean Deoxygenation

Oxygen minimum zones (OMZs) have substantial effects on the global ecology and biogeochemical processes of marine microbes. However, the diversity and activity of OMZ microbes and their trophic interactions are only starting to be documented, especially in regard to the potential roles of viruses and protists. OMZs have expanded over the past 60 years and are predicted to expand due to anthropogenic climate change, furthering the need to understand these regions. This review summarizes the current knowledge of OMZ formation, the biotic and abiotic factors involved in OMZ expansion, and the microbial ecology of OMZs, emphasizing the importance of bacteria, archaea, viruses, and protists. We describe the recognized roles of OMZ microbes in carbon, nitrogen, and sulfur cycling, the potential of viruses in altering host metabolisms involved in these cycles, and the control of microbial populations by grazers and viruses. Further, we highlight the microbial community composition and roles of these organisms in oxic and anoxic depths within the water column and how these differences potentially inform how microbial communities will respond to deoxygenation. Additionally, the current literature on the alteration of microbial communities by other key climate change parameters such as temperature and pH are considered regarding how OMZ microbes might respond to these pressures. Finally, we discuss what knowledge gaps are present in understanding OMZ microbial communities and propose directions that will begin to close these gaps.

Candidatus Thiovulum sp. strain imperiosus: the largest free-living Epsilonproteobacteraeota Thiovulum strain lives in a marine mangrove environment

A large (47.75 ± 3.56 µm in diameter) Thiovulum bacterial strain forming white veils is described from a marine mangrove ecosystem. High sulfide concentrations (up to 8 mM of H2S) were measured on sunken organic matter (wood/bone debris) under laboratory conditions. This sulfur-oxidizing bacterium colonized the organic matter, forming a white veil. According to conventional scanning electron microscope (SEM) observations, bacterial cells are ovoid and slightly motile by numerous small flagella present on the cell surface. Large intracytoplasmic internal sulfur granules were observed, suggesting a sulfidic-based metabolism. Observations were confirmed by elemental sulfur distribution detected by energy-dispersive X-ray spectroscopy (EDXS) analysis using an environmental scanning electron microscope (ESEM) on non-dehydrated samples. Phylogenetic analysis of the partial sequence of 16S rDNA obtained from purified fractions of this Epsilonproteobacteraeota strain indicates that this bacterium belongs to the Thiovulaceae cluster and could be one of the largest Thiovulum ever described. We propose to name this species Candidatus Thiovulum sp. strain imperiosus.

Integrating resilience with functional ecosystem measures: A novel paradigm for management decisions under multiple-stressor interplay in freshwater ecosystems

Moving beyond monitoring the state of water quality to understanding how the sensitive ecosystems "respond" to complex interplay of climatic and anthropogenic perturbations, and eventually the mechanisms that underpin alterations leading to transitional shifts is crucial for managing freshwater resources. The multiple disturbance dynamics-a single disturbance as opposed to multiple disturbances for recovery and other atrocities-alter aquatic ecosystem in multiple ways, yet the global models lack representation of key processes and feedbacks, impeding potential management decisions. Here, the procedure we have embarked for what is known about the biogeochemical and ecological functions in freshwaters in context of ecosystem resilience, feedbacks, stressors synergies, and compensatory dynamics, is highly relevant for process-based ecosystem models and for developing a novel paradigm toward potential management decisions. This review advocates the need for a more aggressive approach with improved understanding of changes in key ecosystem processes and mechanistic links thereof, regulating resilience and compensatory dynamics concordant with climate and anthropogenic perturbations across a wide range of spatio-temporal scales. This has relevance contexting climate change and anthropogenic pressures for developing proactive and adaptive management strategies for safeguarding freshwater resources and services they provide.

The bacterial sulfur cycle in expanding dysoxic and euxinic marine waters

Dysoxic marine waters (DMW, < 1 μM oxygen) are currently expanding in volume in the oceans, which has biogeochemical, ecological and societal consequences on a global scale. In these environments, distinct bacteria drive an active sulfur cycle, which has only recently been recognized for open-ocean DMW. This review summarizes the current knowledge on these sulfur-cycling bacteria. Critical bottlenecks and questions for future research are specifically addressed. Sulfate-reducing bacteria (SRB) are core members of DMW. However, their roles are not entirely clear, and they remain largely uncultured. We found support for their remarkable diversity and taxonomic novelty by mining metagenome-assembled genomes from the Black Sea as model ecosystem. We highlight recent insights into the metabolism of key sulfur-oxidizing SUP05 and Sulfurimonas bacteria, and discuss the probable involvement of uncultivated SAR324 and BS-GSO2 bacteria in sulfur oxidation. Uncultivated Marinimicrobia bacteria with a presumed organoheterotrophic metabolism are abundant in DMW. Like SRB, they may use specific molybdoenzymes to conserve energy from the oxidation, reduction or disproportionation of sulfur cycle intermediates such as S0 and thiosulfate, produced from the oxidation of sulfide. We expect that tailored sampling methods and a renewed focus on cultivation will yield deeper insight into sulfur-cycling bacteria in DMW.

Genome-resolved viral ecology in a marine oxygen minimum zone

Oxygen minimum zones (OMZs) are critical to marine nitrogen cycling and global climate change. While OMZ microbial communities are relatively well-studied, little is known about their viruses. Here, we assess the viral community ecology of 22 deeply sequenced viral metagenomes along a gradient of oxygenated to anoxic waters (<0.02 μmol/l O₂ ) in the Eastern Tropical South Pacific (ETSP) OMZ. We identified 46 127 viral populations (≥5 kb), which augments the known viruses from ETSP by 10-fold. Viral communities clustered into six groups that correspond to oceanographic features. Oxygen concentration was the predominant environmental feature driving viral community structure. Alpha and beta diversity of viral communities in the anoxic zone were lower than in surface waters, which parallels the low microbial diversity seen in other studies. ETSP viruses were largely endemic, with the majority of shared viruses (87%) also present in other OMZ samples. We detected 543 putative viral-encoded auxiliary metabolic genes (AMGs), of which some have a distribution that reflects physico-chemical characteristics across depth. Together these findings provide an ecological baseline for viral community structure, drivers and population variability in OMZs that will help future studies assess the role of viruses in these climate-critical environments.

Viral elements and their potential influence on microbial processes along the permanently stratified Cariaco Basin redoxcline

Little is known about viruses in oxygen-deficient water columns (ODWCs). In surface ocean waters, viruses are known to act as gene vectors among susceptible hosts. Some of these genes may have metabolic functions and are thus termed auxiliary metabolic genes (AMGs). AMGs introduced to new hosts by viruses can enhance viral replication and/or potentially affect biogeochemical cycles by modulating key microbial pathways. Here we identify 748 viral populations that cluster into 94 genera along a vertical geochemical gradient in the Cariaco Basin, a permanently stratified and euxinic ocean basin. The viral communities in this ODWC appear to be relatively novel as 80 of these viral genera contained no reference viral sequences, likely due to the isolation and unique features of this system. We identify viral elements that encode AMGs implicated in distinctive processes, such as sulfur cycling, acetate fermentation, signal transduction, [Fe–S] formation, and N-glycosylation. These AMG-encoding viruses include two putative Mu-like viruses, and viral-like regions that may constitute degraded prophages that have been modified by transposable elements. Our results provide an insight into the ecological and biogeochemical impact of viruses oxygen-depleted and euxinic habitats.

Arcobacter peruensis sp. nov., a Chemolithoheterotroph Isolated from Sulfide- and Organic-Rich Coastal Waters off Peru

Members of the epsilonproteobacterial genus Arcobacter have been identified to be potentially important sulfide oxidizers in marine coastal, seep, and stratified basin environments. In the highly productive upwelling waters off the coast of Peru, Arcobacter cells comprised 3 to 25% of the total microbial community at a near-shore station where sulfide concentrations exceeded 20 μM in bottom waters. From the chemocline where the Arcobacter population exceeded 10⁶ cells ml^-1 and where high rates of denitrification (up to 6.5 ± 0.4 μM N day^-1) and dark carbon fixation (2.8 ± 0.2 μM C day^-1) were measured, we isolated a previously uncultivated Arcobacter species, Arcobacter peruensis sp. nov. (BCCM LMG-31510). Genomic analysis showed that A. peruensis possesses genes encoding sulfide oxidation and denitrification pathways but lacks the ability to fix CO₂ via autotrophic carbon fixation pathways. Genes encoding transporters for organic carbon compounds, however, were present in the A. peruensis genome. Physiological experiments demonstrated that A. peruensis grew best on a mix of sulfide, nitrate, and acetate. Isotope labeling experiments further verified that A. peruensis completely reduced nitrate to N₂ and assimilated acetate but did not fix CO₂, thus coupling heterotrophic growth to sulfide oxidation and denitrification. Single-cell nanoscale secondary ion mass spectrometry analysis of samples taken from shipboard isotope labeling experiments also confirmed that the Arcobacter population in situ did not substantially fix CO₂ The efficient growth yield associated with the chemolithoheterotrophic metabolism of A. peruensis may allow this Arcobacter species to rapidly bloom in eutrophic and sulfide-rich waters off the coast of Peru.IMPORTANCE Our multidisciplinary approach provides new insights into the ecophysiology of a newly isolated environmental Arcobacter species, as well as the physiological flexibility within the Arcobacter genus and sulfide-oxidizing, denitrifying microbial communities within oceanic oxygen minimum zones (OMZs). The chemolithoheterotrophic species Arcobacter peruensis may play a substantial role in the diverse consortium of bacteria that is capable of coupling denitrification and fixed nitrogen loss to sulfide oxidation in eutrophic, sulfidic coastal waters. With increasing anthropogenic pressures on coastal regions, e.g., eutrophication and deoxygenation (D. Breitburg, L. A. Levin, A. Oschlies, M. Grégoire, et al., Science 359:eaam7240, 2018, https://doi.org/10.1126/science.aam7240), niches where sulfide-oxidizing, denitrifying heterotrophs such as A. peruensis thrive are likely to expand.

Comamonadaceae OTU as a Remnant of an Ancient Microbial Community in Sulfidic Waters

Intraterrestrial waters harbor microbial communities being extensively studied to understand microbial processes underlying subsurface ecosystem functioning. This paper provides the results of an investigation on the microbiomes of unique, subsurface sulfidic waters associated with Upper Jurassic, Cretaceous, and Miocene sediments. We used high-throughput 16S rDNA amplicon sequencing to reveal the structure of bacterial and archaeal communities in water samples differing in sulfide content (20-960 mg/dm3), salinity (1.3-3.2%), and depth of extraction (60-660 m below ground level). Composition of the bacterial communities strongly varied across the samples; however, the bacteria participating in the sulfur cycle were common in all sulfidic waters. The shallowest borehole water (60 m bgl) was dominated by sulfur-oxidizing Epsilonproteobacteria (Sulfurimonas, Sulfurovum). In the waters collected from greater depths (148-300 m bgl), the prevalence of Betaproteobacteria (Comamonadaceae) and sulfate/sulfur-reducing Deltaproteobacteria (Desulfopila, Desulfomicrobium, MSBL7) was observed. Sulfate reducers (members of Clostridia: Candidatus Desulforudis) were the most abundant bacteria in the deepest borehole water (660 m bgl). Out of 850 bacterial OTUs, only one, affiliated with the Comamonadaceae family, was found abundant (> 1% of total bacterial sequences) in all samples. Contribution of Archaea to the whole microbial communities was lower than 0.5%. Archaeal communities did not differ across the samples and they consisted of Halobacteriaceae. Out of 372 archaeal OTUs, five, belonging to the four genera Natronomonas, Halorubrum, Halobellus, and Halorhabdus, were the most numerous.

Circumventing kinetics in biogeochemical modeling

Microbial metabolism drives biogeochemical fluxes in virtually every ecosystem. Modeling these fluxes is challenged by the incredible diversity of microorganisms, whose kinetic parameters are largely unknown. In poorly mixed systems, such as stagnant water columns or sediments, however, long-term bulk microbial metabolism may become limited by physical transport rates of substrates across space. Here we mathematically show that under these conditions, biogeochemical fluxes are largely predictable based on the system's transport properties, chemical boundary conditions, and the stoichiometry of metabolic pathways, regardless of the precise kinetics of the resident microorganisms. We formalize these considerations into a predictive modeling framework and demonstrate its use for the Cariaco Basin subeuphotic zone, one of the largest anoxic marine basins worldwide. Using chemical concentration data solely from the upper boundary (depth 180 m) and lower boundary (depth 900 m), but without a priori knowledge of metabolite fluxes, chemical depth profiles, kinetic parameters, or microbial species composition, we predict the concentrations and vertical fluxes of biologically important substances, including oxygen, nitrate, hydrogen sulfide, and ammonium, across the entire considered depth range (180-900 m). Our predictions largely agree with concentration measurements over a period of 14 years ([Formula: see text] = 0.78-0.92) and become particularly accurate during a period where the system was near biogeochemical steady state (years 2007-2009, [Formula: see text] = 0.86-0.95). Our work enables geobiological predictions for a large class of ecosystems without knowledge of kinetic parameters or geochemical depth profiles. Conceptually, our work provides a possible explanation for the decoupling between microbial species composition and bulk metabolic function, observed in various ecosystems.

Contrasting Network Features between Free-Living and Particle-Attached Bacterial Communities in Taihu Lake

Free-living (FL) and particle-attached (PA) bacterial communities play critical roles in nutrient cycles, metabolite production, and as a food source in aquatic systems, and while their community composition, diversity, and functions have been well studied, we know little about their community interactions, co-occurrence patterns, and niche occupancy. In the present study, 13 sites in Taihu Lake were selected to study the differences of co-occurrence patterns and niches occupied between the FL and PA bacterial communities using correlation-based network analysis. The results show that both FL and PA bacterial community networks were non-random and significant differences of the network indexes (average path length, clustering coefficient, modularity) were found between the two groups. Furthermore, the PA bacterial community network consisted of more correlations between fewer OTUs, as well as higher average degree, making it more complex. The results of observed (O) to random (R) ratios of intra- or inter-phyla connections indicate more relationships such as cross-feeding, syntrophic, mutualistic, or competitive relationships in the PA bacterial community network. We also found that four OTUs (OTU00074, OTU00755, OTU00079, and OTU00454), which all had important influences on the nutrients cyclings, played different roles in the two networks as connectors or module hubs. Analysis of the relationships between the module eigengenes and environmental variables demonstrated that bacterial groups of the two networks favored quite different environmental conditions. These findings further confirmed the different ecological functions and niches occupied by the FL and PA bacterial communities in the aquatic ecosystem.

Capturing Compositional Variation in Denitrifying Communities: a Multiple-Primer Approach That Includes Epsilonproteobacteria

Denitrifying Epsilonproteobacteria may dominate nitrogen loss processes in marine habitats with intense redox gradients, but assessment of their importance is limited by the currently available primers for nitrite reductase genes. Nine new primers targeting the nirS gene of denitrifying Epsilonproteobacteria were designed and tested for use in sequencing and quantitative PCR on two microbial mat samples (vent 2 and vent 4) from the Calypso hydrothermal vent field, Bay of Plenty, New Zealand. Commonly used nirS and nirK primer sets nirS1F/nirS6R, cd3aF/R3cd, nirK1F/nirK5R, and F1aCu/R3Cu were also tested to determine what may be missed by the common single-primer approach to assessing denitrifier diversity. The relative importance of Epsilonproteobacteria in these samples was evaluated by 16S rRNA gene sequencing. Epsilonproteobacteria represented up to 75.6% of 16S rRNA libraries, but nirS genes from this group were not found with commonly used primers. Pairing of the new primer EPSnirS511F with either EPSnirS1100R or EPSnirS1105R recovered nirS sequences from members of the genera Sulfurimonas, Sulfurovum, and Nitratifractor. The new quantitative PCR primers EPSnirS103F/EPSnirS530R showed dominance of denitrifying Epsilonproteobacteria in vent 4 compared to vent 2, which had greater representation by "standard" denitrifiers measured with the cd3aF/R3cd primers. Limited results from commonly used nirK primers suggest biased amplification between primers. Future application of multiple nirS and nirK primers, including the new epsilonproteobacterial nirS primers, will improve the detection of denitrifier diversity and the capability to identify changes in dominant denitrifying communities.IMPORTANCE Estimating the potential for increasing nitrogen limitation in the changing global ocean is reliant on understanding the microbial community that removes nitrogen through the process of denitrification. This process is favored under oxygen limitation, which is a growing global-ocean phenomenon. Current methods use the nitrite reductase genes nirS and nirK to assess denitrifier diversity and abundance using primers that target only a few known denitrifiers and systematically exclude denitrifying Epsilonproteobacteria, a group known to dominate in reducing environments, such as hydrothermal vents and anoxic basins. As oxygen depletion expands in the oceans, it is important to study denitrifier community dynamics within those areas to predict future global ocean changes. This study explores the design and testing of new primers that target epsilonproteobacterial nirS and reveals the varied success of existing primers, leading to the recommendation of a multiple-primer approach to assessing denitrifier diversity.

Hypoxia causes preservation of labile organic matter and changes seafloor microbial community composition (Black Sea)

Bottom-water oxygen supply is a key factor governing the biogeochemistry and community composition of marine sediments. Whether it also determines carbon burial rates remains controversial. We investigated the effect of varying oxygen concentrations (170 to 0 μM O₂) on microbial remineralization of organic matter in seafloor sediments and on community diversity of the northwestern Crimean shelf break. This study shows that 50% more organic matter is preserved in surface sediments exposed to hypoxia compared to oxic bottom waters. Hypoxic conditions inhibit bioturbation and decreased remineralization rates even within short periods of a few days. These conditions led to the accumulation of threefold more phytodetritus pigments within 40 years compared to the oxic zone. Bacterial community structure also differed between oxic, hypoxic, and anoxic zones. Functional groups relevant in the degradation of particulate organic matter, such as Flavobacteriia, Gammaproteobacteria, and Deltaproteobacteria, changed with decreasing oxygenation, and the microbial community of the hypoxic zone took longer to degrade similar amounts of deposited reactive matter. We conclude that hypoxic bottom-water conditions-even on short time scales-substantially increase the preservation potential of organic matter because of the negative effects on benthic fauna and particle mixing and by favoring anaerobic processes, including sulfurization of matter.

System-Wide Adaptations of Desulfovibrio alaskensis G20 to Phosphate-Limited Conditions

The prevalence of lipids devoid of phosphorus suggests that the availability of phosphorus limits microbial growth and activity in many anoxic, stratified environments. To better understand the response of anaerobic bacteria to phosphate limitation and starvation, this study combines microscopic and lipid analyses with the measurements of fitness of pooled barcoded transposon mutants of the model sulfate reducing bacterium Desulfovibrio alaskensis G20. Phosphate-limited G20 has lower growth rates and replaces more than 90% of its membrane phospholipids by a mixture of monoglycosyl diacylglycerol (MGDG), glycuronic acid diacylglycerol (GADG) and ornithine lipids, lacks polyphosphate granules, and synthesizes other cellular inclusions. Analyses of pooled and individual mutants reveal the importance of the high-affinity phosphate transport system (the Pst system), PhoR, and glycolipid and ornithine lipid synthases during phosphate limitation. The phosphate-dependent synthesis of MGDG in G20 and the widespread occurrence of the MGDG/GADG synthase among sulfate reducing ∂-Proteobacteria implicate these microbes in the production of abundant MGDG in anaerobic environments where the concentrations of phosphate are lower than 10 μM. Numerous predicted changes in the composition of the cell envelope and systems involved in transport, maintenance of cytoplasmic redox potential, central metabolism and regulatory pathways also suggest an impact of phosphate limitation on the susceptibility of sulfate reducing bacteria to other anthropogenic or environmental stresses.

The Diversity of Sulfide Oxidation and Sulfate Reduction Genes Expressed by the Bacterial Communities of the Cariaco Basin, Venezuela

Qualitative expression of dissimilative sulfite reductase (dsrA), a key gene in sulfate reduction, and sulfide:quinone oxidoreductase (sqr), a key gene in sulfide oxidation was investigated. Neither of the two could be amplified from mRNA retrieved with Niskin bottles but were amplified from mRNA retrieved by the Deep SID. The sqr and sqr-like genes retrieved from the Cariaco Basin were related to the sqr genes from a Bradyrhizobium sp., Methylomicrobium alcaliphilum, Sulfurovum sp. NBC37-1, Sulfurimonas autotrophica, Thiorhodospira sibirica and Chlorobium tepidum. The dsrA gene sequences obtained from the redoxcline of the Cariaco Basin belonged to chemoorganotrophic and chemoautotrophic sulfate and sulfur reducers belonging to the class Deltaproteobacteria (phylum Proteobacteria) and the order Clostridiales (phylum Firmicutes).

Microbial community diversity, structure and assembly across oxygen gradients in meromictic marine lakes, Palau

Microbial communities consume oxygen, alter biogeochemistry and compress habitat in aquatic ecosystems, yet our understanding of these microbial-biogeochemical-ecological interactions is limited by a lack of systematic analyses of low-oxygen ecosystems. Marine lakes provide an ideal comparative system, as they range from well-mixed holomictic lakes to stratified, anoxic, meromictic lakes that vary in their vertical extent of anoxia. We examined microbial communities inhabiting six marine lakes and one ocean site using pyrosequencing of 16S rRNA genes. Microbial richness and evenness was typically highest in the anoxic monimolimnion of meromictic lakes, with common marine bacteria present in mixolimnion communities replaced by anoxygenic phototrophs, sulfate-reducing bacteria and SAR406 in the monimolimnion. These sharp changes in community structure were linked to environmental gradients (constrained variation in redundancy analysis = 68%-76%) - particularly oxygen and pH. However, in those lakes with the steepest oxygen gradients, salinity and dissolved nutrients were important secondary constraining variables, indicating that subtle but substantive differences in microbial communities occur within similar low-oxygen habitats. Deterministic processes were a dominant influence on whole community assembly (all nearest taxon index values >4), demonstrating that the strong environmental gradients present in meromictic marine lakes drive microbial community assembly.

Expanding the World of Marine Bacterial and Archaeal Clades

Determining which microbial taxa are out there, where they live, and what they are doing is a driving approach in marine microbial ecology. The importance of these questions is underlined by concerted, large-scale, and global ocean sampling initiatives, for example the International Census of Marine Microbes, Ocean Sampling Day, or Tara Oceans. Given decades of effort, we know that the large majority of marine Bacteria and Archaea belong to about a dozen phyla. In addition to the classically culturable Bacteria and Archaea, at least 50 “clades,” at different taxonomic depths, exist. These account for the majority of marine microbial diversity, but there is still an underexplored and less abundant portion remaining. We refer to these hitherto unrecognized clades as unknown, as their boundaries, names, and classifications are not available. In this work, we were able to characterize up to 92 of these unknown clades found within the bacterial and archaeal phylogenetic diversity currently reported for marine water column environments. We mined the SILVA 16S rRNA gene datasets for sequences originating from the marine water column. Instead of the usual subjective taxa delineation and nomenclature methods, we applied the candidate taxonomic unit (CTU) circumscription system, along with a standardized nomenclature to the sequences in newly constructed phylogenetic trees. With this new phylogenetic and taxonomic framework, we performed an analysis of ICoMM rRNA gene amplicon datasets to gain insights into the global distribution of the new marine clades, their ecology, biogeography, and interaction with oceanographic variables. Most of the new clades we identified were interspersed by known taxa with cultivated members, whose genome sequences are available. This result encouraged us to perform metabolic predictions for the novel marine clades using the PICRUSt approach. Our work also provides an update on the taxonomy of several phyla and widely known marine clades as our CTU approach breaks down these randomly lumped clades into smaller objectively calculated subgroups. Finally, all taxa were classified and named following standards compatible with the Bacteriological Code rules, enhancing their digitization, and comparability with future microbial ecological and taxonomy studies.

Microbial diversity and activity in the Nematostella vectensis holobiont: insights from 16S rRNA gene sequencing, isolate genomes, and a pilot-scale survey of gene expression

We have characterized the molecular and genomic diversity of the microbiota of the starlet sea anemone Nematostella vectensis, a cnidarian model for comparative developmental and functional biology and a year-round inhabitant of temperate salt marshes. Molecular phylogenetic analysis of 16S rRNA gene clone libraries revealed four ribotypes associated with N. vectensis at multiple locations and times. These associates include two novel ribotypes within the ε-Proteobacterial order Campylobacterales and the Spirochetes, respectively, each sharing <85% identity with cultivated strains, and two γ-Proteobacterial ribotypes sharing >99% 16S rRNA identity with Endozoicomonas elysicola and Pseudomonas oleovorans, respectively. Species-specific PCR revealed that these populations persisted in N. vectensis asexually propagated under laboratory conditions. cDNA indicated expression of the Campylobacterales and Endozoicomonas 16S rRNA in anemones from Sippewissett Marsh, MA. A collection of bacteria from laboratory raised N. vectensis was dominated by isolates from P. oleovorans and Rhizobium radiobacter. Isolates from field-collected anemones revealed an association with Limnobacter and Stappia isolates. Genomic DNA sequencing was carried out on 10 cultured bacterial isolates representing field- and laboratory-associates, i.e., Limnobacter spp., Stappia spp., P. oleovorans and R. radiobacter. Genomes contained multiple genes identified as virulence (host-association) factors while S. stellulata and L. thiooxidans genomes revealed pathways for mixotrophic sulfur oxidation. A pilot metatranscriptome of laboratory-raised N. vectensis was compared to the isolate genomes and indicated expression of ORFs from L. thiooxidans with predicted functions of motility, nutrient scavenging (Fe and P), polyhydroxyalkanoate synthesis for carbon storage, and selective permeability (porins). We hypothesize that such activities may mediate acclimation and persistence of bacteria in a N. vectensis holobiont defined by both internal and external gradients of chemicals and nutrients in a dynamic coastal habitat.

A Dissolved Oxygen Threshold for Shifts in Bacterial Community Structure in a Seasonally Hypoxic Estuary

Pelagic ecosystems can become depleted of dissolved oxygen as a result of both natural processes and anthropogenic effects. As dissolved oxygen concentration decreases, energy shifts from macrofauna to microorganisms, which persist in these hypoxic zones. Oxygen-limited regions are rapidly expanding globally; however, patterns of microbial communities associated with dissolved oxygen gradients are not yet well understood. To assess the effects of decreasing dissolved oxygen on bacteria, we examined shifts in bacterial community structure over space and time in Hood Canal, Washington, USA−a glacial fjord-like water body that experiences seasonal low dissolved oxygen levels known to be detrimental to fish and other marine organisms. We found a strong negative association between bacterial richness and dissolved oxygen. Bacterial community composition across all samples was also strongly associated with the dissolved oxygen gradient, and significant changes in bacterial community composition occurred at a dissolved oxygen concentration between 5.18 and 7.12 mg O₂ L^-1. This threshold value of dissolved oxygen is higher than classic definitions of hypoxia (<2.0 mg O₂ L^-1), suggesting that changes in bacterial communities may precede the detrimental effects on ecologically and economically important macrofauna. Furthermore, bacterial taxa responsible for driving whole community changes across the oxygen gradient are commonly detected in other oxygen-stressed ecosystems, suggesting that the patterns we uncovered in Hood Canal may be relevant in other low oxygen ecosystems.

The dynamics of the bacterial diversity in the redox transition and anoxic zones of the Cariaco Basin assessed by parallel tag sequencing

Massively parallel tag sequencing was applied to describe the bacterial diversity in the redox transition and anoxic zones of the Cariaco Basin. In total, 14 samples from the Cariaco Basin were collected over a period of eight years from two stations. A total of 244 357 unique bacterial V6 amplicons were sequenced. The total number of operational taxonomic units (OTUs) found in this study was 4692, with a range of 511-1491 OTUs per sample. Approximately 95% of the OTUs found in the redox transition zone and anoxic layers of Cariaco are represented by less than 50 amplicons suggesting that only about 5% of the bacterial OTUs are responsible for the bulk of the microbial processes in the basin redox transition and anoxic zones. The same dominant OTUs were observed across all eight years of sampling although periodic fluctuations in their proportion were apparent. No distinctive differences were observed between the bacterial communities from the redox transition and anoxic layers of the Cariaco Basin water column. The largest proportion of amplicons belongs to Gammaproteobacteria represented mostly by sulfide oxidizers, followed by Marine Group A (originally described as SAR406; Gordon and Giovannoni 1996), a group of uncultured bacteria hypothesized to be involved in metal reduction, and sulfate-reducing Deltaproteobacteria. Gammaproteobacteria, Deltaproteobacteria and Marine Group A make up 67-90% of all V6 amplicons sequenced in this study. This strongly suggests that the basin's microbial communities are actively involved in the sulfur-related metabolism and coupling of the sulfur and carbon cycles. According to detrended canonical correspondence analysis, ecological factors such as chemoautotrophy, nitrate and oxidized and reduced sulfur compounds influence the structuring and distribution of the Cariaco microbial communities.

Global patterns of abundance, diversity and community structure of the Aminicenantes (candidate phylum OP8)

We investigated the global patterns of abundance, diversity, and community structure of members of the Aminicenantes (candidate phylum OP8). Our aim was to identify the putative ecological role(s) played by members of this poorly characterized bacterial lineages in various ecosystems. Analysis of near full-length 16S rRNA genes identified four classes and eight orders within the Aminicenantes. Within 3,134 datasets comprising ∼1.8 billion high throughput-generated partial 16S rRNA genes, 47,351 Aminicenantes-affiliated sequences were identified in 913 datasets. The Aminicenantes exhibited the highest relative abundance in hydrocarbon-impacted environments, followed by marine habitats (especially hydrothermal vents and coral-associated microbiome samples), and aquatic, non-marine habitats (especially in terrestrial springs and groundwater samples). While the overall abundance of the Aminicenantes was higher in low oxygen tension as well as non-saline and low salinity habitats, it was encountered in a wide range of oxygen tension, salinities, and temperatures. Analysis of the community structure of the Aminicenantes showed distinct patterns across various datasets that appear to be, mostly, driven by habitat variations rather than prevalent environmental parameters. We argue that the detection of the Aminicenantes across environmental extremes and the observed distinct community structure patterns reflect a high level of intraphylum metabolic diversity and adaptive capabilities that enable its survival and growth in a wide range of habitats and environmental conditions.

Composition and variation of sediment bacterial and nirS-harboring bacterial communities at representative sites of the Bohai Gulf coastal zone, China

With rapid urbanization, anthropogenic activities are increasingly influencing the natural environment of the Bohai Bay. In this study, the composition and variation of bacterial and nirS-harboring bacterial communities in the coastal zone sediments of the Bohai Gulf were analyzed using PCR-based clone libraries. A total of 95 genera were detected in the bacterial communities, with Proteobacteria (72.1 %), Acidobacteria (10.5 %), Firmicutes (1.7 %), Bacteroidetes (1.4 %), Chloroflexi (0.7 %) and Planctomycetes (0.7 %) being the dominated phyla. The NirS sequences were divided into nine Clusters (A-I). Canonical correlation analysis showed that the bacterial or denitrifying communities were correlated with different environmental factors, such as total organic carbon, total nitrogen, ammonium, sulfate, etc. Furthermore, bacterial communities' composition and diversity are influenced by oil exploration, sewage discharge and other anthropogenic activities in the coastal area of the Bohai Sea. Thus, this study provided useful information on further research on regional or global environmental control and restore.

Ultradeep 16S rRNA sequencing analysis of geographically similar but diverse unexplored marine samples reveal varied bacterial community composition

Background

Bacterial community composition in the marine environment differs from one geographical location to another. Reports that delineate the bacterial diversity of different marine samples from geographically similar location are limited. The present study aims to understand whether the bacterial community compositions from different marine samples harbour similar bacterial diversity since these are geographically related to each other.

Methods and Principal Findings

In the present study, 16S rRNA deep sequencing analysis targeting V3 region was performed using Illumina bar coded sequencing. A total of 22.44 million paired end reads were obtained from the metagenomic DNA of Marine sediment, Rhizosphere sediment, Seawater and the epibacterial DNA of Seaweed and Seagrass. Diversity index analysis revealed that Marine sediment has the highest bacterial diversity and the least bacterial diversity was observed in Rhizosphere sediment. Proteobacteria, Actinobacteria and Bacteroidetes were the dominant taxa present in all the marine samples. Nearly 62–71% of rare species were identified in all the samples and most of these rare species were unique to a particular sample. Further taxonomic assignment at the phylum and genus level revealed that the bacterial community compositions differ among the samples.

Conclusion

This is the first report that supports the fact that, bacterial community composition is specific for specific samples irrespective of its similar geographical location. Existence of specific bacterial community for each sample may drive overall difference in bacterial structural composition of each sample. Further studies like whole metagenomic sequencing will throw more insights to the key stone players and its interconnecting metabolic pathways. In addition, this is one of the very few reports that depicts the unexplored bacterial diversity of marine samples (Marine sediment, Rhizosphere sediment, Seawater) and the host associated marine samples (Seaweed and Seagrass) at higher depths from uncharacterised coastal region of Palk Bay, India using next generation sequencing technology.

Genomic properties of Marine Group A bacteria indicate a role in the marine sulfur cycle

Marine Group A (MGA) is a deeply branching and uncultivated phylum of bacteria. Although their functional roles remain elusive, MGA subgroups are particularly abundant and diverse in oxygen minimum zones and permanent or seasonally stratified anoxic basins, suggesting metabolic adaptation to oxygen-deficiency. Here, we expand a previous survey of MGA diversity in O₂-deficient waters of the Northeast subarctic Pacific Ocean (NESAP) to include Saanich Inlet (SI), an anoxic fjord with seasonal O₂ gradients and periodic sulfide accumulation. Phylogenetic analysis of small subunit ribosomal RNA (16S rRNA) gene clone libraries recovered five previously described MGA subgroups and defined three novel subgroups (SHBH1141, SHBH391, and SHAN400) in SI. To discern the functional properties of MGA residing along gradients of O₂ in the NESAP and SI, we identified and sequenced to completion 14 fosmids harboring MGA-associated 16S RNA genes from a collection of 46 fosmid libraries sourced from NESAP and SI waters. Comparative analysis of these fosmids, in addition to four publicly available MGA-associated large-insert DNA fragments from Hawaii Ocean Time-series and Monterey Bay, revealed widespread genomic differentiation proximal to the ribosomal RNA operon that did not consistently reflect subgroup partitioning patterns observed in 16S rRNA gene clone libraries. Predicted protein-coding genes associated with adaptation to O₂-deficiency and sulfur-based energy metabolism were detected on multiple fosmids, including polysulfide reductase (psrABC), implicated in dissimilatory polysulfide reduction to hydrogen sulfide and dissimilatory sulfur oxidation. These results posit a potential role for specific MGA subgroups in the marine sulfur cycle.

Identification of bacteria in enrichment cultures of sulfate reducers in the Cariaco Basin water column employing Denaturing Gradient Gel Electrophoresis of 16S ribosomal RNA gene fragments

BACKGROUND

The Cariaco Basin is characterized by pronounced and predictable vertical layering of microbial communities dominated by reduced sulfur species at and below the redox transition zone. Marine water samples were collected in May, 2005 and 2006, at the sampling stations A (10°30' N, 64°40' W), B (10°40' N, 64°45' W) and D (10°43'N, 64°32'W) from different depths, including surface, redox interface, and anoxic zones. In order to enrich for sulfate reducing bacteria (SRB), water samples were inoculated into anaerobic media amended with lactate or acetate as carbon source. To analyze the composition of enrichment cultures, we performed DNA extraction, PCR-DGGE, and sequencing of selected bands.

RESULTS

DGGE results indicate that many bacterial genera were present that are associated with the sulfur cycle, including Desulfovibrio spp., as well as heterotrophs belonging to Vibrio, Enterobacter, Shewanella, Fusobacterium, Marinifilum, Mariniliabilia, and Spirochaeta. These bacterial populations are related to sulfur coupling and carbon cycles in an environment of variable redox conditions and oxygen availability.

CONCLUSIONS

In our studies, we found an association of SRB-like Desulfovibrio with Vibrio species and other genera that have a previously defined relevant role in sulfur transformation and coupling of carbon and sulfur cycles in an environment where there are variable redox conditions and oxygen availability. This study provides new information about microbial species that were culturable on media for SRB at anaerobic conditions at several locations and water depths in the Cariaco Basin.

Methanobrevibacter boviskoreani sp. nov., isolated from the rumen of Korean native cattle

Three strictly anaerobic, methanogenic strains JH1(T), JH4 and JH8 were isolated from rumen of the Korean native cattle (HanWoo; Bos taurus coreanae) in South Korea. The colonies were circular, opaque, and slightly yellowish. Phylogenetic analyses of 16S rRNA gene and mcrA (encoding α subunit of methyl-coenzyme M reductase) sequences confirmed the affiliation of the novel strains with the Methanobacteriales, and Methanobrevibacter wolinii SH(T) was the most closely related species. The 16S rRNA gene and mcrA sequence similarities between strains JH1(T), JH4 and JH8 and M. wolinii SH(T) were 96.2 and 89.0 % respectively, and DNA-DNA hybridization of the isolates and M. wolinii DSM 11976(T) showed a 20 % reassociation. Strain JH1(T) exhibited 92 % DNA-DNA relatedness with strains JH4 and JH8, and their 16S rRNA gene and mcrA sequences were identical. Cells stained Gram-positive and were non-motile rods, 1.5-1.8 µm long and 0.6 µm wide. The strains were able to use H2/CO2 and formate. The optimum temperature and pH ranges for growth were 37-40 °C and pH 6.5-7.0. The DNA G+C content of strain JH1(T) was 28 mol%. Based on data from this study using a polyphasic approach, the three strains represent a novel species of genus Methanobrevibacter, for which the name Methanobrevibacter boviskoreani sp. nov. is proposed. The type strain is JH1(T) ( = KCTC 4102(T) = JCM 18376(T)).

Oscillibacter ruminantium sp. nov., isolated from the rumen of Korean native cattle

A strictly anaerobic, Gram-negative, non-spore-forming bacterium, designated GH1T, was isolated from the rumen of Korean native cattle (HanWoo). Cells were straight to slightly curved rods (2.0–4.5 µm long) and were motile by peritrichous flagella. The isolate grew at 30–45 °C (optimum 40 °C), at pH 5.5–6.5 (optimum pH 6.0) and with up to 3.5 % (w/v) NaCl. Strain GH1T produced acid from d-glucose, d-ribose and d-xylose, with butyric acid being the major end product. The genomic DNA G+C content was 54.6 mol%. Based on comparative 16S rRNA gene sequence analysis, strain GH1T was most closely related to Oscillibacter valericigenes Sjm18-20T (97.3 % 16S rRNA gene sequence similarity). DNA–DNA hybridization between strain GH1T and O. valericigenes DSM 18026T showed 24 % reassociation. The major fatty acids were iso-C13 : 0 (13.0 %), iso-C15 : 0 (17.6 %), anteiso-C15 : 0 (8.4 %) and C14 : 0 (4.1 %), and the cellular fatty acid methyl esters as dimethylacetals (DMAs) were C16 : 0 DMA (17.8 %), iso-C15 : 0 DMA (15.2 %) and C14 : 0 DMA (4.52 %). The cell-wall peptidoglycan of strain GH1T contained meso-diaminopimelic acid and the major cell-wall sugar was galactose. Based on 16S rRNA gene sequence similarity, phylogenetic analysis, DNA G+C content, DNA–DNA relatedness and distinct phenotypic characteristics, strain GH1T is classified in the genus Oscillibacter as a member of a novel species, for which the name Oscillibacter ruminantium sp. nov. is proposed. The type strain is GH1T ( = KCTC 15176T = NBRC 108824T = JCM 18333T).

The microbiology of deep-sea hydrothermal vent plumes: ecological and biogeographic linkages to seafloor and water column habitats

Hydrothermal plumes are an important yet understudied component of deep-sea vent microbial ecosystems. The significance of plume microbial processes can be appreciated from three perspectives: (1) mediation of plume biogeochemistry, (2) dispersal of seafloor hydrothermal vent microbes between vents sites, (3) as natural laboratories for understanding the ecology, physiology, and function of microbial groups that are distributed throughout the pelagic deep sea. Plume microbiology has been largely neglected in recent years, especially relative to the extensive research conducted on seafloor and subseafloor systems. Rapidly advancing technologies for investigating microbial communities provide new motivation and opportunities to characterize this important microbial habitat. Here we briefly highlight microbial contributions to plume and broader ocean (bio)geochemistry and review recent work to illustrate the ecological and biogeographic linkages between plumes, seafloor vent habitats, and other marine habitats such as oxygen minimum zones (OMZs), cold seeps, and oil spills. 16S rRNA gene surveys and metagenomic/-transcriptomic data from plumes point to dominant microbial populations, genes, and functions that are also operative in OMZs (SUP05, ammonia-oxidizing Archaea, and SAR324 Deltaproteobacteria) and hydrocarbon-rich environments (methanotrophs). Plume microbial communities are distinct from those on the seafloor or in the subsurface but contain some signatures of these habitats, consistent with the notion that plumes are potential vectors for dispersal of microorganisms between seafloor vent sites. Finally, we put forward three pressing questions for the future of deep-sea hydrothermal plume research and consider interactions between vents and oceans on global scales.

Acetate-utilizing bacteria at an oxic-anoxic interface in the Baltic Sea

Pelagic redoxclines represent chemical gradients of elevated microbial activities. While chemolithoautotrophic microorganisms in these systems are well known as catalysts of major biogeochemical cycles, comparable knowledge on heterotrophic organisms is scarce. Thus, in this study, identity and biogeochemical involvement of active heterotrophs were investigated in stimulation experiments and activity measurements based on samples collected from pelagic redoxclines of the central Baltic Sea in 2005 and 2009. In the 2009 samples, (13)C-acetate 16S rRNA stable isotope probing (16S rRNA-SIP) identified gammaproteobacteria affiliated with Colwellia sp. and Neptunomonas sp. in addition to epsilonproteobacteria related to Arcobacter spp. as active heterotrophs at the oxic-anoxic interface layer. Incubations from sulfidic waters were dominated by two phylogenetic subgroups of Arcobacter. In the 2005 samples, organics, manganese(IV), and iron(III) were added to the sulfidic waters, followed by the determination of metal reduction and identification of the stimulated organisms. Here, the same Arcobacter and Colwellia subgroups were stimulated as in 2009, with Arcobacter predominating in samples, in which manganese(IV) reduction was highest. Our results offer new insights into the heterotrophic bacterial assemblage of Baltic Sea pelagic redoxclines and suggest Arcobacter spp. as a heterotroph with presumed relevance also for manganese cycling.

Bacterial community composition in a large marine anoxic basin: a Cariaco Basin time-series survey

Redox transition zones play a crucial role in biogeochemical cycles of several major elements. Because microorganisms mediate many reactions of these cycles, they actively participate in establishing geochemical gradients. In turn, the geochemical gradients structure microbial communities. We studied the interrelationship between the bacterial community structure and the geochemical gradient in the Cariaco Basin, the largest truly marine anoxic basin. This study's dataset includes bacterial community composition in 113 water column samples as well as the data for environmental variables (gradients of oxygen, hydrogen sulfide, sulfite, thiosulfate, ammonia, nitrate, nitrite, dissolved manganese and iron, dark CO2 fixation, and bacterial abundance) collected between 1997 and 2006. Several prominent bacterial groups are present throughout the entire water column. These include members of Gamma-, Delta-, and Epsilonproteobacteria, as well as members of the Marine Group A, the candidate divisions OP11 and Car731c. Canonical correspondence analysis indicated that microbial communities segregate along vectors representing oxygenated conditions, nitrite, nitrate and anoxic environments represented by chemoautotrophy, ammonia, sulfite, and hydrogen sulfide.

Microbial diversity in the deep-subsurface hydrothermal aquifer feeding the giant gypsum crystal-bearing Naica Mine, Mexico

The Naica Mine in northern Mexico is famous for its giant gypsum crystals, which may reach up to 11 m long and contain fluid inclusions that might have captured microorganisms during their formation. These crystals formed under particularly stable geochemical conditions in cavities filled by low salinity hydrothermal water at 54-58°C. We have explored the microbial diversity associated to these deep, saline hydrothermal waters collected in the deepest (ca. 700-760 m) mineshafts by amplifying, cloning and sequencing small-subunit ribosomal RNA genes using primers specific for archaea, bacteria, and eukaryotes. Eukaryotes were not detectable in the samples and the prokaryotic diversity identified was very low. Two archaeal operational taxonomic units (OTUs) were detected in one sample. They clustered with, respectively, basal Thaumarchaeota lineages and with a large clade of environmental sequences branching at the base of the Thermoplasmatales within the Euryarchaeota. Bacterial sequences belonged to the Candidate Division OP3, Firmicutes and the Alpha- and Beta-proteobacteria. Most of the lineages detected appear autochthonous to the Naica system, since they had as closest representatives environmental sequences retrieved from deep sediments or the deep subsurface. In addition, the high GC content of 16S rRNA gene sequences belonging to the archaea and to some OP3 OTUs suggests that at least these lineages are thermophilic. Attempts to amplify diagnostic functional genes for methanogenesis (mcrA) and sulfate reduction (dsrAB) were unsuccessful, suggesting that those activities, if present, are not important in the aquifer. By contrast, genes encoding archaeal ammonium monooxygenase (AamoA) were amplified, suggesting that Naica Thaumarchaeota are involved in nitrification. These organisms are likely thermophilic chemolithoautotrophs adapted to thrive in an extremely energy-limited environment.

Diversity and population structure of Marine Group A bacteria in the Northeast subarctic Pacific Ocean

Marine Group A (MGA) is a candidate phylum of Bacteria that is ubiquitous and abundant in the ocean. Despite being prevalent, the structural and functional properties of MGA populations remain poorly constrained. Here, we quantified MGA diversity and population structure in relation to nutrients and O₂ concentrations in the oxygen minimum zone (OMZ) of the Northeast subarctic Pacific Ocean using a combination of catalyzed reporter deposition fluorescence in situ hybridization (CARD-FISH) and 16S small subunit ribosomal RNA (16S rRNA) gene sequencing (clone libraries and 454-pyrotags). Estimates of MGA abundance as a proportion of total bacteria were similar across all three methods although estimates based on CARD-FISH were consistently lower in the OMZ (5.6%±1.9%) than estimates based on 16S rRNA gene clone libraries (11.0%±3.9%) or pyrotags (9.9%±1.8%). Five previously defined MGA subgroups were recovered in 16S rRNA gene clone libraries and five novel subgroups were defined (HF770D10, P262000D03, P41300E03, P262000N21 and A714018). Rarefaction analysis of pyrotag data indicated that the ultimate richness of MGA was very nearly sampled. Spearman's rank analysis of MGA abundances by CARD-FISH and O₂ concentrations resulted in significant correlation. Analyzed in more detail by 16S rRNA pyrotag sequencing, MGA operational taxonomic units affiliated with subgroups Arctic95A-2 and A714018 comprised 0.3–2.4% of total bacterial sequences and displayed strong correlations with decreasing O₂ concentration. This study is the first comprehensive description of MGA diversity using complementary techniques. These results provide a phylogenetic framework for interpreting future studies on ecotype selection among MGA subgroups, and suggest a potentially important role for MGA in the ecology and biogeochemistry of OMZs.

Vertical distribution of microbial communities in a perennially stratified Arctic lake with saline, anoxic bottom waters

Meromictic lakes are useful biogeochemical models because of their stratified chemical gradients and separation of redox reactions down the water column. Perennially ice-covered meromictic lakes are particularly stable, with long term constancy in their density profiles. Here we sampled Lake A, a deep meromictic lake at latitude 83°N in High Arctic Canada. Sampling was before (May) and after (August) an unusual ice-out event during the warm 2008 summer. We determined the bacterial and archaeal community composition by high-throughput 16S rRNA gene tag-pyrosequencing. Both prokaryote communities were stratified by depth and the Bacteria differed between dates, indicating locally driven selection processes. We matched taxa to known taxon-specific biogeochemical functions and found a close correspondence between the depth of functional specialists and chemical gradients. These results indicate a rich microbial diversity despite the extreme location, with pronounced vertical structure in taxonomic and potential functional composition, and with community shifts during ice-out.

Three manganese oxide-rich marine sediments harbor similar communities of acetate-oxidizing manganese-reducing bacteria

Dissimilatory manganese reduction dominates anaerobic carbon oxidation in marine sediments with high manganese oxide concentrations, but the microorganisms responsible for this process are largely unknown. In this study, the acetate-utilizing manganese-reducing microbiota in geographically well-separated, manganese oxide-rich sediments from Gullmar Fjord (Sweden), Skagerrak (Norway) and Ulleung Basin (Korea) were analyzed by 16S rRNA-stable isotope probing (SIP). Manganese reduction was the prevailing terminal electron-accepting process in anoxic incubations of surface sediments, and even the addition of acetate stimulated neither iron nor sulfate reduction. The three geographically distinct sediments harbored surprisingly similar communities of acetate-utilizing manganese-reducing bacteria: 16S rRNA of members of the genera Colwellia and Arcobacter and of novel genera within the Oceanospirillaceae and Alteromonadales were detected in heavy RNA-SIP fractions from these three sediments. Most probable number (MPN) analysis yielded up to 10(6) acetate-utilizing manganese-reducing cells cm(-3) in Gullmar Fjord sediment. A 16S rRNA gene clone library that was established from the highest MPN dilutions was dominated by sequences of Colwellia and Arcobacter species and members of the Oceanospirillaceae, supporting the obtained RNA-SIP results. In conclusion, these findings strongly suggest that (i) acetate-dependent manganese reduction in manganese oxide-rich sediments is catalyzed by members of taxa (Arcobacter, Colwellia and Oceanospirillaceae) previously not known to possess this physiological function, (ii) similar acetate-utilizing manganese reducers thrive in geographically distinct regions and (iii) the identified manganese reducers differ greatly from the extensively explored iron reducers in marine sediments.

Convergent development of anodic bacterial communities in microbial fuel cells

Microbial fuel cells (MFCs) are often inoculated from a single wastewater source. The extent that the inoculum affects community development or power production is unknown. The stable anodic microbial communities in MFCs were examined using three inocula: a wastewater treatment plant sample known to produce consistent power densities, a second wastewater treatment plant sample, and an anaerobic bog sediment. The bog-inoculated MFCs initially produced higher power densities than the wastewater-inoculated MFCs, but after 20 cycles all MFCs on average converged to similar voltages (470±20 mV) and maximum power densities (590±170 mW m⁻²). The power output from replicate bog-inoculated MFCs was not significantly different, but one wastewater-inoculated MFC (UAJA3 (UAJA, University Area Joint Authority Wastewater Treatment Plant)) produced substantially less power. Denaturing gradient gel electrophoresis profiling showed a stable exoelectrogenic biofilm community in all samples after 11 cycles. After 16 cycles the predominance of Geobacter spp. in anode communities was identified using 16S rRNA gene clone libraries (58±10%), fluorescent in-situ hybridization (FISH) (63±6%) and pyrosequencing (81±4%). While the clone library analysis for the underperforming UAJA3 had a significantly lower percentage of Geobacter spp. sequences (36%), suggesting that a predominance of this microbe was needed for convergent power densities, the lower percentage of this species was not verified by FISH or pyrosequencing analyses. These results show that the predominance of Geobacter spp. in acetate-fed systems was consistent with good MFC performance and independent of the inoculum source.

Dissimilatory sulfur cycling in oxygen minimum zones: an emerging metagenomics perspective

Biological diversity in marine OMZs (oxygen minimum zones) is dominated by a complex community of bacteria and archaea whose anaerobic metabolisms mediate key steps in global nitrogen and carbon cycles. Molecular and physiological studies now confirm that OMZs also support diverse micro-organisms capable of utilizing inorganic sulfur compounds for energy metabolism. The present review focuses specifically on recent metagenomic data that have helped to identify the molecular basis for autotrophic sulfur oxidation with nitrate in the OMZ water column, as well as a cryptic role for heterotrophic sulfate reduction. Interpreted alongside marker gene surveys and process rate measurements, these data suggest an active sulfur cycle with potentially substantial roles in organic carbon input and mineralization and critical links to the OMZ nitrogen cycle. Furthermore, these studies have created a framework for comparing the genomic diversity and ecology of pelagic sulfur-metabolizing communities from diverse low-oxygen regions.

Microbial diversity of an anoxic zone of a hydroelectric power station reservoir in Brazilian Amazonia

Microbial diversity was evaluated in an anoxic zone of Tucuruí Hydroelectric Power Station reservoir in Brazilian Amazonia using a culture-independent approach by amplifying and sequencing fragments of the 16S rRNA gene using metagenomic DNA as a template. Samples obtained from the photic, aphotic (40 m) and sediment (60 m) layers were used to construct six 16S rDNA libraries containing a total of 1,152 clones. The sediment, aphotic and photic layers presented 64, 33 and 35 unique archaeal operational taxonomic units (OTUs). The estimated richness of these layers was evaluated to be 153, 106 and 79 archaeal OTUs, respectively, using the abundance-based coverage estimator (ACE) and 114, 83 and 77 OTUs using the Chao1 estimator. For bacterial sequences, 114, 69 and 57 OTUs were found in the sediment, aphotic and photic layers, which presented estimated richnesses of 1,414, 522 and 197 OTUs (ACE) and 1,059, 1,014 and 148 OTUs (Chao1), respectively. Phylogenetic analyses of the sequences obtained revealed a high richness of microorganisms which participate in the carbon cycle, namely, methanogenic archaea and methanotrophic proteobacteria. Most sequences obtained belong to non-culturable prokaryotes. The present study offers the first glimpse of the huge microbial diversity of an anoxic area of a man-made lacustrine environment in the tropics.

Single-cell analysis reveals a novel uncultivated magnetotactic bacterium within the candidate division OP3

Magnetotactic bacteria (MTB) are a diverse group of prokaryotes that orient along magnetic fields using membrane-coated magnetic nanocrystals of magnetite (Fe(3) O(4) ) or greigite (Fe(3) S(4) ), the magnetosomes. Previous phylogenetic analysis of MTB has been limited to few cultivated species and most abundant members of natural populations, which were assigned to Proteobacteria and the Nitrospirae phyla. Here, we describe a single cell-based approach that allowed the targeted phylogenetic and ultrastructural analysis of the magnetotactic bacterium SKK-01, which was low abundant in sediments of Lake Chiemsee. Morphologically conspicuous single cells of SKK-01 were micromanipulated from magnetically collected multi-species MTB populations, which was followed by whole genome amplification and ultrastructural analysis of sorted cells. Besides intracellular sulphur inclusions, the large ovoid cells of SKK-01 harbour ∼175 bullet-shaped magnetosomes arranged in multiple chains that consist of magnetite as revealed by TEM and EDX analysis. Sequence analysis of 16 and 23S rRNA genes from amplified genomic DNA as well as fluorescence in situ hybridization assigned SKK-01 to the candidate division OP3, which so far lacks any cultivated representatives. SKK-01 represents the first morphotype that can be assigned to the OP3 group as well as the first magnetotactic member of the PVC superphylum.

Vertical distribution of Archaea and Bacteria in a meromictic lake as determined by fluorescent in situ hybridization

The prokaryotic cells distribution in the water column of the coastal saline meromictic Lake Faro (Messina, Italy) was investigated by microscopic counting techniques. Water samples were collected at a central station from the surface to the bottom, when waters were characterized by a marked stratification. A "red-water" layer, caused by a dense growth of photosynthetic sulfur bacteria, was present at a depth of 15 m, defining a transition area between oxic (mixolimnion) and anoxic (monimolimnion) layers. Fluorescently labeled 16S rRNA oligonucleotide, group-specific probes were used to determine the abundance of Bacteria and Archaea, and their subgroups, Green Sulfur Bacteria (GSB), Sulfate Reducing Bacteria (SRB), Cyanobacteria and Chromatium okenii, and Crenarchaeota and Euryarchaeota, as key elements of the microbial community. Bacteria decreased from surface to bottom, while Archaea increased with depth and reached the maximum value at 30 m, where they outnumbered the Bacteria. Bacteria and picophytoplankton prevailed in the mixolimnion. At the chemocline high numbers of prokaryotic cells were present, mainly represented by Cyanobacteria, Chromatium okenii and Euryarchaeota. GSB, SRB, and Crenarchaeota prevailed below the chemocline. Although Archaea constitute a minor fraction of microbial community, they could represent active contributors to the meromictic Lake Faro ecosystem.

Temporal distribution of the archaeal community in the Changjiang Estuary hypoxia area and the adjacent East China Sea as determined by denaturing gradient gel electrophoresis and multivariate analysis

The archaeal community and the effects of environmental factors on microbial community distribution were investigated at five sampling sites in the Changjiang Estuary hypoxia area and the adjacent East China Sea in June, August, and October 2006. Profiles of the archaeal communities were generated by denaturing gradient gel electrophoresis of 16S rRNA genes followed by DNA sequence analysis, and the results were analyzed by multivariate statistical analysis. Denaturing gradient gel electrophoresis band patterns were analyzed by cluster analysis to assess temporal changes in the genetic diversity of the archaeal communities. Most of the October samples grouped together separately from those of June and August. Analysis of DNA sequences revealed that the dominant archaeal groups in the Changjiang Estuary hypoxia area and the adjacent East China Sea were affiliated with Euryarchaeota (mainly marine group II) and Crenarchaeota. The effects of environmental factors on the archaeal community distribution were analyzed by the ordination technique of canonical correspondence analysis. Salinity had a significant effect on the archaeal community composition.

Global patterns of bacterial beta-diversity in seafloor and seawater ecosystems

Background

Marine microbial communities have been essential contributors to global biomass, nutrient cycling, and biodiversity since the early history of Earth, but so far their community distribution patterns remain unknown in most marine ecosystems.

Methodology/Principal Findings

The synthesis of 9.6 million bacterial V6-rRNA amplicons for 509 samples that span the global ocean's surface to the deep-sea floor shows that pelagic and benthic communities greatly differ, at all taxonomic levels, and share <10% bacterial types defined at 3% sequence similarity level. Surface and deep water, coastal and open ocean, and anoxic and oxic ecosystems host distinct communities that reflect productivity, land influences and other environmental constraints such as oxygen availability. The high variability of bacterial community composition specific to vent and coastal ecosystems reflects the heterogeneity and dynamic nature of these habitats. Both pelagic and benthic bacterial community distributions correlate with surface water productivity, reflecting the coupling between both realms by particle export. Also, differences in physical mixing may play a fundamental role in the distribution patterns of marine bacteria, as benthic communities showed a higher dissimilarity with increasing distance than pelagic communities.

Conclusions/Significance

This first synthesis of global bacterial distribution across different ecosystems of the World's oceans shows remarkable horizontal and vertical large-scale patterns in bacterial communities. This opens interesting perspectives for the definition of biogeographical biomes for bacteria of ocean waters and the seabed.

Abundance and phylogenetic identity of archaeoplankton in the permanent oxygen minimum zone of the eastern tropical South Pacific

We assessed the abundance and molecular phylogeny of archaeoplankton in the oxygen minimum zone (OMZ) of the eastern tropical South Pacific, using specific-probe hybridization and phylogenetic analysis of the SSU-rRNA gene. Euryarchaea from Marine Group-II (MG-II) were most abundant in the surface oxic layer, representing 4.0±2.0% of the total picoplankton, while crenarchaea from Group I.1a (G-I.1a) peaked at the oxyclines, with a relative abundance of 8.1±4.3% (upper oxycline). In most of the stations, the abundance of both the groups decreased at the core of the OMZ, where a secondary maximum in cell density is commonly observed. The majority of the phylotypes affiliated with one of three groups: MG-II, euryarchaeal Marine Group-III (MG-III) and G-I.1a (75.9%, 12.8% and 10.3%, respectively). While MG-II phylotypes were found throughout the water column and G-I.1a ones were predominantly found within the oxyclines, MG-III phylotypes came almost exclusively from the OMZ core. Higher archaeal richness was found within the OMZ, with some of the exclusive lineages grouping with sequences from the deep ocean and hydrothermal vents. Moreover, G-I.1a sequences from the OMZ grouped into a different subcluster from the aerobic ammonium-oxidizer Nitrosopumilus maritimus. Thus, the community structure of archaeoplankton in OMZs is rich and distinct, with G-I.1a members particularly prominent at the oxyclines.