Diverse, uncultivated bacteria and archaea underlying the cycling of dissolved protein in the ocean

Transcriptional activity differentiates families of Marine Group II Euryarchaeota in the coastal ocean

Marine Group II Euryarchaeota (Candidatus Poseidoniales), abundant but yet-uncultivated members of marine microbial communities, are thought to be (photo)heterotrophs that metabolize dissolved organic matter (DOM), such as lipids and peptides. However, little is known about their transcriptional activity. We mapped reads from a metatranscriptomic time series collected at Sapelo Island (GA, USA) to metagenome-assembled genomes to determine the diversity of transcriptionally active Ca. Poseidoniales. Summer metatranscriptomes had the highest abundance of Ca. Poseidoniales transcripts, mostly from the O1 and O3 genera within Ca. Thalassarchaeaceae (MGIIb). In contrast, transcripts from fall and winter samples were predominantly from Ca. Poseidoniaceae (MGIIa). Genes encoding proteorhodopsin, membrane-bound pyrophosphatase, peptidase/proteases, and part of the ß-oxidation pathway were highly transcribed across abundant genera. Highly transcribed genes specific to Ca. Thalassarchaeaceae included xanthine/uracil permease and receptors for amino acid transporters. Enrichment of Ca. Thalassarchaeaceae transcript reads related to protein/peptide, nucleic acid, and amino acid transport and metabolism, as well as transcript depletion during dark incubations, provided further evidence of heterotrophic metabolism. Quantitative PCR analysis of South Atlantic Bight samples indicated consistently abundant Ca. Poseidoniales in nearshore and inshore waters. Together, our data suggest that Ca. Thalassarchaeaceae are important photoheterotrophs potentially linking DOM and nitrogen cycling in coastal waters.

Marine Group-II archaea dominate particle-attached as well as free-living archaeal assemblages in the surface waters of Kongsfjorden, Svalbard, Arctic Ocean

Marine archaea are a significant component of the global oceanic ecosystems, including the polar oceans. However, only a few attempts have been made to study archaea in the high Arctic fjords. Given the importance of Archaea in carbon and nitrogen cycling, it is imperative to explore their diversity and community composition in the high Arctic fjords, such as Kongsfjorden (Svalbard). In the present study, we evaluated archaeal diversity and community composition in the size-fractionated microbial population, viz-a-viz free-living (FL; 0.2-3 μm) and particle-attached (PA; > 3 μm) using archaeal V3-V4 16S rRNA gene amplicon sequencing. Our results indicate that the overall archaeal community in the surface water of Kongsfjorden was dominated by the members of the marine group-II (MGII) archaea, followed by the MGI group members, including Nitrosopumilaceae and Nitrososphaeraceae. Although a clear niche partitioning between PA and FL archaeal communities was not observed, 2 OTUs among 682 OTUs, and 3 ASVs out of 1932 ASVs were differentially abundant among the fractions. OTU001/ASV0002, classified as MGIIa, was differentially abundant in the PA fraction. OTU006/ASV0006/ASV0010 affiliated with MGIIb were differentially abundant in the FL fraction. Particulate organic nitrogen and C:N ratio were the most significant variables (P < 0.05) explaining the observed variation in the FL and PA archaeal communities, respectively. These results indicate an exchange between archaeal communities or a generalist lifestyle switching between FL and PA fractions. Besides, the particles' elemental composition (carbon and nitrogen) seems to play an essential role in shaping the PA archaeal communities in the surface waters of Kongsfjorden.

Anaerobic bacterial degradation of protein and lipid macromolecules in subarctic marine sediment

Microorganisms in marine sediments play major roles in marine biogeochemical cycles by mineralizing substantial quantities of organic matter from decaying cells. Proteins and lipids are abundant components of necromass, yet the taxonomic identities of microorganisms that actively degrade them remain poorly resolved. Here, we revealed identities, trophic interactions, and genomic features of bacteria that degraded 13C-labeled proteins and lipids in cold anoxic microcosms containing sulfidic subarctic marine sediment. Supplemented proteins and lipids were rapidly fermented to various volatile fatty acids within 5 days. DNA-stable isotope probing (SIP) suggested Psychrilyobacter atlanticus was an important primary degrader of proteins, and Psychromonas members were important primary degraders of both proteins and lipids. Closely related Psychromonas populations, as represented by distinct 16S rRNA gene variants, differentially utilized either proteins or lipids. DNA-SIP also showed 13C-labeling of various Deltaproteobacteria within 10 days, indicating trophic transfer of carbon to putative sulfate-reducers. Metagenome-assembled genomes revealed the primary hydrolyzers encoded secreted peptidases or lipases, and enzymes for catabolism of protein or lipid degradation products. Psychromonas species are prevalent in diverse marine sediments, suggesting they are important players in organic carbon processing in situ. Together, this study provides new insights into the identities, functions, and genomes of bacteria that actively degrade abundant necromass macromolecules in the seafloor.

Accumulation of detached kelp biomass in a subtidal temperate coastal ecosystem induces succession of epiphytic and sediment bacterial communities

Kelps are dominant primary producers in temperate coastal ecosystems. Large amounts of kelp biomass can be exported to the seafloor during the algal growth cycle or following storms, creating new ecological niches for the associated microbiota. Here, we investigated the bacterial community associated with the kelp Laminaria hyperborea during its accumulation and degradation on the seafloor. Kelp tissue, seawater and sediment were sampled during a 6-month in situ experiment simulating kelp detritus accumulation. Evaluation of the epiphytic bacterial community abundance, structure, taxonomic composition and predicted functional profiles evidenced a biphasic succession. Initially, dominant genera (Hellea, Litorimonas, Granulosicoccus) showed a rapid and drastic decrease in sequence abundance, probably outcompeted by algal polysaccharide-degraders such as Bacteroidia members which responded within 4 weeks. Acidimicrobiia, especially members of the Sva0996 marine group, colonized the degrading kelp biomass after 11 weeks. These secondary colonizers could act as opportunistic scavenger bacteria assimilating substrates exposed by early degraders. In parallel, kelp accumulation modified bacterial communities in the underlying sediment, notably favouring anaerobic taxa potentially involved in the sulfur and nitrogen cycles. Overall, this study provides insights into the bacterial degradation of algal biomass in situ, an important link in coastal trophic chains.

Primary role of increasing urea-N concentration in a novel Microcystis densa bloom: Evidence from ten years of field investigations and laboratory experiments

A novel Microcystis bloom caused by Microcystis densa has occurred in a typical subtropical reservoir every spring and summer since 2012, and it has caused several ecological and economic losses. To determine the environmental factors that influence the growth and physiological characteristics of M. densa, we investigated the variations in physicochemical factors and M. densa cell density from 2007 to 2017. The results showed that the urea-N concentration increased significantly (from 0.02 ± 0.00-0.20 ± 0.01 mg N l^-1), whereas other factors did not vary significantly. NO₃^--N and urea-N concentrations were higher than the NH₄⁺-N concentration during the M. densa bloom. The nitrogen composition changed, and urea-N and NO₃^--N became a major nitrogen sources in the reservoir. Water temperature and increased urea-N concentrations were the primary factors that influenced variations in M. densa cell density (45.5%, p < 0.05). Laboratory experiments demonstrated that M. densa cultured with urea-N exhibited a higher maximum cell density (9.8 ± 0.5 × 10⁸ cells l^-1), more cellular pigments for photosynthesis (chlorophyll a and phycocyanin) and photoprotection (carotenoid), and more proteins than those cultured with NH₄⁺-N and NO₃^--N. These results suggested that M. densa cultured with urea-N exhibited preferable growth and physiological conditions. Moreover, M. densa exhibited an increased maximum specific uptake rate (0.93 pg N cell^-1 h^-1) and reduced half-saturation constant (0.03 mg N l^-1) for urea-N compared with NH₄⁺-N and NO₃^--N, suggesting that M. densa preferred urea-N as its major nitrogen source. These results collectively indicated that the increasing urea-N concentration was beneficial for the growth and physiological conditions of M. densa. This study provided ten years of field data and detailed physiological information supporting the critical effect of urea-N on the growth of a novel bloom species M. densa. These findings helped to reveal the mechanism of M. densa bloom formation from the perspective of dissolved organic nitrogen.

Experimental evidence for long-term coexistence of copiotrophic and oligotrophic bacteria in pelagic surface seawater

Most marine copiotrophic bacteria can produce extracellular enzymes to degrade biopolymers into bio-available smaller solutes, while oligotrophic bacteria usually cannot. Bacterial extracellular enzymes and enzymatic products can be a common resource that could be utilized by both copiotrophs and oligotrophs; when present, oligotrophs may outcompete the enzyme-producing copiotrophs. However, copiotrophs and oligotrophs consistently coexist in the ocean. How they maintain coexistence has still not been experimentally studied. In this study, the interaction and coexistence of a copiotroph and an oligotroph, isolated from the same surface seawater sample and utilizing the same proteinaceous substrate, were experimentally investigated. The copiotroph could secrete extracellular proteases to degrade and then utilize the proteinaceous substrate. The oligotroph was unable to utilize the proteinaceous substrate by itself, but could grow by using the hydrolysate amino acids. The copiotroph outcompeted the oligotroph by adsorbing the amino acids quickly and having a higher growth rate in the rich medium. The oligotroph survived by adapting to low concentration of nutrients. The copiotroph and oligotroph were able to maintain long-term (up to 142 days) coexistence in the laboratory. This study indicates that differences in the utilization of different concentrations of nutrients can drive the coexistence of marine copiotrophs and oligotrophs.

A Large-Scale Survey of the Bacterial Communities in Lakes of Western Mongolia with Varying Salinity Regimes

In recent years, climate change coupled with anthropogenic activities has led to monumental changes in saline lakes which are rapidly drying up across the globe and particularly in Central Asia. The landlocked country of Mongolia is rich in lakes which have remained primarily undisturbed by human impact, and many of these lakes have varying salinity regimes and are located across various geographical landscapes. In this study, we sampled 18 lakes with varying salinity regimes (hyperhaline, mesohaline, oligohaline, and polyhaline) covering 7000 km of western Mongolia and its various geographical landscapes (Gobi Desert, forests, and steppe). We identified that the bacterial communities that dominate these lakes are significantly influenced by salinity (p < 0.001) and geographical landscape (p < 0.001). Further, only five zOTUs were shared in all the lakes across the salinity regimes, providing evidence that both local and regional factors govern the community assembly and composition. Furthermore, the bacterial communities of hyperhaline lakes were significantly positively correlated with salinity (ANOVA, p < 0.001) and arsenic concentrations (ANOVA, p < 0.001), whereas bacterial communities of mesohaline and polyhaline lakes situated in forest and steppe landscapes were positively correlated with temperature (ANOVA, p < 0.001) and altitude (ANOVA, p < 0.001), respectively. Functional predictions based on the 16S rRNA gene indicated enrichment of KEGG Ontology terms related to transporters for osmoprotection and -regulation. Overall, our study provides a comprehensive view of the bacterial diversity and community composition present in these lakes, which might be lost in the future.

Distinct Distribution of Archaea From Soil to Freshwater to Estuary: Implications of Archaeal Composition and Function in Different Environments

In addition to inhabiting extreme territories, Archaea are widely distributed in common environments spanning from terrestrial to aquatic environments. This study investigated and compared archaeal community structures from three different habitats (representing distinct environments): agriculture soils (from farming system trials FST, PA, United States), freshwater biofilms (from White Clay Creek, PA, United States), and estuary water (Chesapeake Bay, United States). High-throughput sequencing of 16S rRNA genes indicated that Thaumarchaeota, Euryarchaeota, Nanoarchaeota, Crenarchaeota, and Diapherotrites were the commonly found dominant phyla across these three environments. Similar to Bacteria, distinct community structure and distribution patterns for Archaea were observed in soils vs. freshwater vs. estuary. However, the abundance, richness, evenness, and diversity of archaeal communities were significantly greater in soils than it was in freshwater and estuarine environments. Indicator species (or amplicon sequence variants, ASVs) were identified from different nitrogen and carbon cycling archaeal groups in soils (Nitrososphaerales, Nitrosotaleales, Nitrosopumilales, Methanomassiliicoccales, Lainarchaeales), freshwater biofilms (Methanobacteria, Nitrososphaerales) and Chesapeake Bay (Marine Group II, Nitrosopumilales), suggesting the habitat-specificity of their biogeochemical contributions to different environments. Distinct functional aspects of Archaea were also confirmed by functional predictions (PICRUSt2 analysis). Further, co-occurrence network analysis indicated that only soil Archaea formed stable modules. Keystone species (ASVs) were identified mainly from Methanomassiliicoccales, Nitrososphaerales, Nitrosopumilales. Overall, these results indicate a strong habitat-dependent distribution of Archaea and their functional partitions within the local environments.

Fecal indicator bacteria, direct pathogen detection, and microbial community analysis provide different microbiological water quality assessment of a tropical urban marine estuary

Urban marine estuaries are often impacted by microbiological contamination that impairs use and affects human health acutely, while limited is known about microbiological water quality in urban marine estuaries in the absence of reported sewage spills. This study used a tropical urban marine estuary, the Ala Wai Canal in Honolulu, Hawaii, as the model system to compare fecal indicator bacteria (FIB) concentrations, bacterial pathogen profiles, and microbial community structures. The FIB Escherichia coli exhibited higher geometric mean 132 CFU/100mL (n=28) than those of enterococci (18 CFU/100mL) and Clostridium perfringens (21 CFU/100mL). Amongst the four pathogens targeted by cultivation methods (Salmonella, Campylobacter, Listeria monocytogenes and Vibrio parahaemolyticus), only was V. parahaemolyticus detected and was detected at high frequency. Microbial community analysis through 16S rRNA gene amplicon sequencing also indicated the high prevalence of Vibrio in the water. The pathogen detection patterns and microbial community structure showed no significant correlation with FIB concentration profiles. Together, the results highlight the limitation of using traditional FIB in assessing water microbiological quality in the tropical urban marine estuary environment, indicating the need for more comprehensive microbial risk assessment approaches such as direct detection of pathogens.

Stable Isotope Probing Identifies Bacterioplankton Lineages Capable of Utilizing Dissolved Organic Matter Across a Range of Bioavailability

Bacterioplankton consume about half of the dissolved organic matter (DOM) produced by phytoplankton. DOM released from phytoplankton consists of a myriad of compounds that span a range of biological reactivity from labile to recalcitrant. Linking specific bacterioplankton lineages to the incorporation of DOM compounds into biomass is important to understand microbial niche partitioning. We conducted a series of DNA-stable isotope probing (SIP) experiments using ¹³C-labeled substrates of varying lability including amino acids, cyanobacteria lysate, and DOM from diatom and cyanobacteria isolates concentrated on solid phase extraction PPL columns (SPE-DOM). Amendments of substrates into Sargasso Sea bacterioplankton communities were conducted to explore microbial response and DNA-SIP was used to determine which lineages of Bacteria and Archaea were responsible for uptake and incorporation. Greater increases in bacterioplankton abundance and DOC removal were observed in incubations amended with cyanobacteria-derived lysate and amino acids compared to the SPE-DOM, suggesting that the latter retained proportionally more recalcitrant DOM compounds. DOM across a range of bioavailability was utilized by diverse prokaryotic taxa with copiotrophs becoming the most abundant ¹³C-incorporating taxa in the amino acid treatment and oligotrophs becoming the most abundant ¹³C-incorporating taxa in SPE-DOM treatments. The lineages that responded to SPE-DOM amendments were also prevalent in the mesopelagic of the Sargasso Sea, suggesting that PPL extraction of phytoplankton-derived DOM isolates compounds of ecological relevance to oligotrophic heterotrophic bacterioplankton. Our study indicates that DOM quality is an important factor controlling the diversity of the microbial community response, providing insights into the roles of different bacterioplankton in resource exploitation and efficiency of marine carbon cycling.

Labile Dissolved Organic Matter Compound Characteristics Select for Divergence in Marine Bacterial Activity and Transcription

Bacteria play a key role in the planetary carbon cycle partly because they rapidly assimilate labile dissolved organic matter (DOM) in the ocean. However, knowledge of the molecular mechanisms at work when bacterioplankton metabolize distinct components of the DOM pool is still limited. We, therefore, conducted seawater culture enrichment experiments with ecologically relevant DOM, combining both polymer and monomer model compounds for distinct compound classes. This included carbohydrates (polysaccharides vs. monosaccharides), proteins (polypeptides vs. amino acids), and nucleic acids (DNA vs. nucleotides). We noted pronounced changes in bacterial growth, activity, and transcription related to DOM characteristics. Transcriptional responses differed between compound classes, with distinct gene sets (“core genes”) distinguishing carbohydrates, proteins, and nucleic acids. Moreover, we found a strong divergence in functional transcription at the level of particular monomers and polymers (i.e., the condensation state), primarily in the carbohydrates and protein compound classes. These specific responses included a variety of cellular and metabolic processes that were mediated by distinct bacterial taxa, suggesting pronounced functional partitioning of organic matter. Collectively, our findings show that two important facets of DOM, compound class and condensation state, shape bacterial gene expression, and ultimately select for distinct bacterial (functional) groups. This emphasizes the interdependency of marine bacteria and labile carbon compounds for regulating the transformation of DOM in surface waters.

Patterns in microbiome composition differ with ocean acidification in anatomic compartments of the Mediterranean coral Astroides calycularis living at CO2 vents

Coral microbiomes, the complex microbial communities associated with the different anatomic compartments of the coral, provide important functions for the host's survival, such as nutrient cycling at the host's surface, prevention of pathogens colonization, and promotion of nutrient uptake. Microbiomes are generally referred to as plastic entities, able to adapt their composition and functionality in response to environmental change, with a possible impact on coral acclimatization to phenomena related to climate change, such as ocean acidification. Ocean sites characterized by natural gradients of pCO₂ provide models for investigating the ability of marine organisms to acclimatize to decreasing seawater pH. Here we compared the microbiome of the temperate, shallow water, non-symbiotic solitary coral Astroides calycularis that naturally lives at a volcanic CO₂ vent in Ischia Island (Naples, Italy), with that of corals living in non-acidified sites at the same island. Bacterial DNA associated with the different anatomic compartments (mucus, tissue and skeleton) of A. calycularis was differentially extracted and a total of 68 samples were analyzed by 16S rRNA gene sequencing. In terms of phylogenetic composition, the microbiomes associated with the different coral anatomic compartments were different from each other and from the microbial communities of the surrounding seawater. Of all the anatomic compartments, the mucus-associated microbiome differed the most between the control and acidified sites. The differences detected in the microbial communities associated to the three anatomic compartments included a general increase in subdominant bacterial groups, some of which are known to be involved in different stages of the nitrogen cycle, such as potential nitrogen fixing bacteria and bacteria able to degrade organic nitrogen. Our data therefore suggests a potential increase of nitrogen fixation and recycling in A. calycularis living close to the CO₂ vent system.

Differential Responses of a Coastal Prokaryotic Community to Phytoplanktonic Organic Matter Derived from Cellular Components and Exudates

The phytoplanktonic production and prokaryotic consumption of organic matter significantly contribute to marine carbon cycling. Organic matter released from phytoplankton via three processes (exudation of living cells, cell disruption through grazing, and viral lysis) shows distinct chemical properties. We herein investigated the effects of phytoplanktonic whole-cell fractions (WF) (representing cell disruption by grazing) and extracellular fractions (EF) (representing exudates) prepared from Heterosigma akashiwo, a bloom-forming Raphidophyceae, on prokaryotic communities using culture-based experiments. We analyzed prokaryotic community changes for two weeks. The shift in cell abundance by both treatments showed similar dynamics, reaching the first peak (~4.1×10⁶‍ ‍cells‍ ‍mL^–1) on day 3 and second peak (~1.1×10⁶‍ ‍cells‍ ‍mL^–1) on day 13. We classified the sequences obtained into operational taxonomic units (OTUs). A Bray-Curtis dissimilarity analysis revealed that the OTU-level community structure changed distinctively with the two treatments. Ten and 13 OTUs were specifically abundant in the WF and EF treatments, respectively. These OTUs were assigned as heterotrophic bacteria mainly belonging to the Alteromonadales (Gammaproteobacteria) and Bacteroidetes clades and showed successive dynamics following the addition of organic matter. We also analyzed the dynamics of these OTUs in the ocean using publicly available metagenomic data from a natural coastal bloom in Monterey Bay, USA. At least two WF treatment OTUs showed co-occurrence with H. akashiwo, indicating that the blooms of H. akashiwo also affect these OTUs in the ocean. The present results strongly suggest that the thriving and dead cells of uninfected phytoplankton differentially influence the marine prokaryotic community.

Impact of sea level change on coastal soil organic matter, priming effects and prokaryotic community assembly

Salt marshes are coastal areas storing high amounts of soil organic matter (SOM) while simultaneously being prone to tidal changes. Here, SOM-decomposition and accompanied priming effects (PE), which describe interactions between labile and old SOM, were studied under controlled flooding conditions. Soil samples from two Wadden Sea salt marsh zones, pioneer (Pio), flooded two times/day, and lower salt marsh (Low), flooded ∼eight times/month, were measured for 56 days concerning CO2-efflux and prokaryotic community shifts during three different inundation-treatments: total-drained (Drained), all-time-flooded (Waterlogged) or temporal-flooding (Tidal). Priming was induced by 14C-glucose addition. CO2-efflux from soil followed Low>Pio and Tidal>Drained>Waterlogged, likely due to O2-depletion and moisture maintenance, two key factors governed by tidal inundation with regard to SOM mineralisation. PEs in both zones were positive (Drained) or absent (Waterlogged, Tidal), presumably as a result of prokaryotes switching from production of extracellular enzymes to direct incorporation of labile C. A doubled amount of prokaryotic biomass in Low compared to Pio probably induced higher chances of cometabolic effects and higher PE. 16S-rRNA-gene-amplicon-based analysis revealed differences in bacterial and archaeal community composition between both zones, revealing temporal niche adaptation with flooding treatment. Strongest alterations were found in Drained, likely due to inundation-mediated changes in C-binding capacities.

Modelling Free-Living and Particle-Associated Bacterial Assemblages across the Deep and Hypoxic Lower St. Lawrence Estuary

The Estuary and Gulf of St. Lawrence (EGSL) in eastern Canada is an appealing ecosystem for studying how microbial communities and metabolic processes are related to environmental change. Ocean and climate variability result in large spatiotemporal variations in environmental conditions and oceanographic processes. The EGSL is also exposed to a variety of additional human pressures that threaten its integrity and sustainable use, including shipping, aquiculture, coastal development, and oil exploration. To monitor and perhaps mitigate the impacts of these human activities on the EGSL, a comprehensive understanding of the biological communities is required. In this study, we provide the first comprehensive view of bacterial diversity in the EGSL and describe the distinct bacterial assemblages associated with different environmental habitats. This work therefore provides an important baseline ecological framework for bacterial communities in the EGSL useful for further studies on how these communities may respond to environmental change.

The Estuary and Gulf of St. Lawrence (EGSL) in eastern Canada are among the largest and most productive coastal ecosystems in the world. Very little information on bacterial diversity exists, hampering our understanding of the relationships between bacterial community structure and biogeochemical function in the EGSL. During the productive spring period, we investigated free-living and particle-associated bacterial communities across the stratified waters of the Lower St. Lawrence Estuary, including the particle-rich surface and bottom boundary layers. Modelling of community structure based on 16S rRNA gene and transcript diversity identified bacterial assemblages specifically associated with four habitat types defined by water mass (upper water or lower water column) and size fraction (free living or particle associated). Assemblages from the upper waters represent sets of cooccurring bacterial populations that are widely distributed across Lower St. Lawrence Estuary surface waters and likely key contributors to organic matter degradation during the spring. In addition, we provide strong evidence that particles in deep hypoxic waters and the bottom boundary layer support a metabolically active bacterial community that is compositionally distinct from those of surface particles and the free-living communities. Among the distinctive features of the bacterial assemblage associated with lower-water particles was the presence of uncultivated lineages of Deltaproteobacteria, including marine myxobacteria. Overall, these results provide an important ecological framework for further investigations of the biogeochemical contributions of bacterial populations in this important coastal marine ecosystem.

IMPORTANCE The Estuary and Gulf of St. Lawrence (EGSL) in eastern Canada is an appealing ecosystem for studying how microbial communities and metabolic processes are related to environmental change. Ocean and climate variability result in large spatiotemporal variations in environmental conditions and oceanographic processes. The EGSL is also exposed to a variety of additional human pressures that threaten its integrity and sustainable use, including shipping, aquiculture, coastal development, and oil exploration. To monitor and perhaps mitigate the impacts of these human activities on the EGSL, a comprehensive understanding of the biological communities is required. In this study, we provide the first comprehensive view of bacterial diversity in the EGSL and describe the distinct bacterial assemblages associated with different environmental habitats. This work therefore provides an important baseline ecological framework for bacterial communities in the EGSL useful for further studies on how these communities may respond to environmental change.

Diversity, ecology and evolution of Archaea

Compared to bacteria, our knowledge of archaeal biology is limited. Historically, microbiologists have mostly relied on culturing and single-gene diversity surveys to understand Archaea in nature. However, only six of the 27 currently proposed archaeal phyla have cultured representatives. Advances in genomic sequencing and computational approaches are revolutionizing our understanding of Archaea. The recovery of genomes belonging to uncultured groups from the environment has resulted in the description of several new phyla, many of which are globally distributed and are among the predominant organisms on the planet. In this Review, we discuss how these genomes, together with long-term enrichment studies and elegant in situ measurements, are providing insights into the metabolic capabilities of the Archaea. We also debate how such studies reveal how important Archaea are in mediating an array of ecological processes, including global carbon and nutrient cycles, and how this increase in archaeal diversity has expanded our view of the tree of life and early archaeal evolution, and has provided new insights into the origin of eukaryotes.

Insights on comparative bacterial diversity between different arid zones of Cholistan Desert, Pakistan

The present study was conducted to analyze bacterial diversity profile of Cholistan desert located in Pakistan. The study investigates the influence of physicochemical parameters of soil on distribution of different bacteria at all taxonomic levels and also study the distribution pattern between different desert environments, particularly rhizospheric and bulk desert sands. Species richness showed phyla Proteobacteria and Chloroflexi as the dominant OTUs in all the samples. Besides the two phyla, the rhizospheric soils with root remnants were dominated by Firmicutes, Deinococcus-Thermus, Actinobacteria and Acidobacteri, while phylum Thermotogae was present in significant quantity in rhizosheaths devoid of roots. In non-rhizospheric desert soils, a considerable number of OTUs belonged to phyla Proteobacteria, Chloroflexi, Bacteroidetes and Acidobacteria. An important finding from this study is that a bulk portion of the OTUs were assigned to unclassified taxa, indicating a large repertoire of unexplored taxa in the desert ecology of Pakistan. Distribution of taxonomic groups among various regions of the desert was collaborating well with the physicochemical parameters of the sites. The findings of this study establish the fundamental relationships between desert ecosystem, specific native plant and the total bacterial flora. This is the first study of microbial community analysis of any desert in Pakistan and thus, will serve as a future platform to explore further on desert ecosystem functioning by employing the ever-changing biotechnological tools.

DNA stable-isotope probing reveals potential key players for microbial decomposition and degradation of diatom-derived marine particulate matter

Microbially mediated decomposition of particulate organic carbon (POC) is a central component of the oceanic carbon cycle, controlling the flux of organic carbon from the surface ocean to the deep ocean. Yet, the specific microbial taxa responsible for POC decomposition and degradation in the deep ocean are still unknown. To target the active microbial lineages involved in these processes, ¹³ C-labeled particulate organic matter (POM) was used as a substrate to incubate particle-attached (PAM) and free-living microbial (FLM) assemblages from the epi- and bathypelagic zones of the New Britain Trench (NBT). By combining DNA stable-isotope probing and Illumina Miseq high-throughput sequencing of bacterial 16S rRNA gene, we identified 14 active bacterial taxonomic groups that implicated in the decomposition of ¹³ C-labeled POM at low and high pressures under the temperature of 15°C. Our results show that both PAM and FLM were able to decompose POC and assimilate the released DOC. However, similar bacterial taxa in both the PAM and FLM assemblages were involved in POC decomposition and DOC degradation, suggesting the decoupling between microbial lifestyles and ecological functions. Microbial decomposition of POC and degradation of DOC were accomplished primarily by particle-attached bacteria at atmospheric pressure and by free-living bacteria at high pressures. Overall, the POC degradation rates were higher at atmospheric pressure (0.1 MPa) than at high pressures (20 and 40 MPa) under 15°C. Our results provide direct evidence linking the specific particle-attached and free-living bacterial lineages to decomposition and degradation of diatomic detritus at low and high pressures and identified the potential mediators of POC fluxes in the epi- and bathypelagic zones.

Polysaccharide niche partitioning of distinct Polaribacter clades during North Sea spring algal blooms

Massive releases of organic substrates during marine algal blooms trigger growth of many clades of heterotrophic bacteria. Algal polysaccharides represent the most diverse and structurally complex class of these substrates, yet their role in shaping the microbial community composition is poorly understood. We investigated, whether polysaccharide utilization capabilities contribute to niche differentiation of Polaribacter spp. (class Flavobacteriia; known to include relevant polysaccharide-degraders) that were abundant during 2009–2012 spring algal blooms in the southern North Sea. We identified six distinct Polaribacter clades using phylogenetic and phylogenomic analyses, quantified their abundances via fluorescence in situ hybridization, compared metagenome-assembled genomes, and assessed in situ gene expression using metaproteomics. Four clades with distinct polysaccharide niches were dominating. Polaribacter 2-a comprised typical first responders featuring small genomes with limited polysaccharide utilization capacities. Polaribacter 3-a were abundant only in 2010 and possessed a distinct sulfated α-glucoronomannan degradation potential. Polaribacter 3-b responded late in blooms and had the capacity to utilize sulfated xylan. Polaribacter 1-a featured high numbers of glycan degradation genes and were particularly abundant following Chattonella algae blooms. These results support the hypothesis that sympatric Polaribacter clades occupy distinct glycan niches during North Sea spring algal blooms.

Host identity and symbiotic association affects the taxonomic and functional diversity of the clownfish-hosting sea anemone microbiome

All eukaryotic life engages in symbioses with a diverse community of bacteria that are essential for performing basic life functions. In many cases, eukaryotic organisms form additional symbioses with other macroscopic eukaryotes. The tightly linked physical interactions that characterize many macroscopic symbioses create opportunities for microbial transfer, which likely affects the diversity and function of individual microbiomes, and may ultimately lead to microbiome convergence between distantly related taxa. Here, we sequence the microbiomes of five species of clownfish-hosting sea anemones that co-occur on coral reefs in the Maldives. We test the importance of evolutionary history, clownfish symbiont association, and habitat on the taxonomic and predicted functional diversity of the microbiome, and explore signals of microbiome convergence in anemone taxa that have evolved symbioses with clownfishes independently. Our data indicate that host identity and clownfish association shapes the majority of the taxonomic diversity of the clownfish-hosting sea anemone microbiome, and predicted functional microbial diversity analyses demonstrate a convergence among host anemone microbiomes, which reflect increased functional diversity over individuals that do not host clownfishes. Further, we identify upregulated predicted microbial functions that are likely affected by clownfish presence. Taken together our study potentially reveals an even deeper metabolic coupling between clownfishes and their host anemones, and what could be a previously unknown mutualistic benefit to anemones that are symbiotic with clownfishes.

Spatio-temporal insights into microbiology of the freshwater-to-hypersaline, oxic-hypoxic-euxinic waters of Ursu Lake

Ursu Lake is located in the Middle Miocene salt deposit of Central Romania. It is stratified, and the water column has three distinct water masses: an upper freshwater-to-moderately saline stratum (0-3 m), an intermediate stratum exhibiting a steep halocline (3-3.5 m), and a lower hypersaline stratum (4 m and below) that is euxinic (i.e. anoxic and sulphidic). Recent studies have characterized the lake's microbial taxonomy and given rise to intriguing ecological questions. Here, we explore whether the communities are dynamic or stable in relation to taxonomic composition, geochemistry, biophysics, and ecophysiological functions during the annual cycle. We found: (i) seasonally fluctuating, light-dependent communities in the upper layer (≥0.987-0.990 water-activity), a stable but phylogenetically diverse population of heterotrophs in the hypersaline stratum (water activities down to 0.762) and a persistent plate of green sulphur bacteria that connects these two (0.958-0.956 water activity) at 3-3.5 to 4 m; (ii) communities that might be involved in carbon- and sulphur-cycling between and within the lake's three main water masses; (iii) uncultured lineages including Acetothermia (OP1), Cloacimonetes (WWE1), Marinimicrobia (SAR406), Omnitrophicaeota (OP3), Parcubacteria (OD1) and other Candidate Phyla Radiation bacteria, and SR1 in the hypersaline stratum (likely involved in the anaerobic steps of carbon- and sulphur-cycling); and (iv) that species richness and habitat stability are associated with high redox-potentials. Ursu Lake has a unique and complex ecology, at the same time exhibiting dynamic fluctuations and stability, and can be used as a modern analogue for ancient euxinic water bodies and comparator system for other stratified hypersaline systems.

Diversity of Bacterial Community in the Oxygen Minimum Zones of Arabian Sea and Bay of Bengal as Deduced by Illumina Sequencing

The Indian Ocean harbors oxygen minimum zones (OMZs) in the Arabian Sea and Bay of Bengal, with dissolved oxygen < 20 μM, located at the mid-depths of the water column. Till date, high-throughput sequence-data on depth-wise distribution of prokaryotic communities have rarely been reported from these OMZs. The present study aimed to characterize the prokaryotic diversity inhabiting Arabian Sea Time Series (ASTS) and India's Idea 2 (II2) in the Arabian Sea, and Bay of Bengal Time Series (BoBTS) in the Bay of Bengal OMZs based on amplicon sequencing of 16S rRNA gene regions, along six sampled depths in the water column. High prokaryotic richness was observed in the Arabian Sea and Bay of Bengal samples. Operational taxonomic units (OTUs) in the range of 1249-3298 were identified, wherein, less prokaryotic diversity was observed at surface and within oxygen minimum depths. At phylum level, most OTUs were affiliated to Bacteroidetes, Chloroflexi, Cyanobacteria, Marinimicrobia, Planctomycetes, and Proteobacteria. Prokaryotic community differed between ASTS, II2 and BoBTS locations along varying physicochemical conditions. Predictive functional profiling of the bacterial communities suggested the involvement of abundant microbes in nitrogen and sulfur metabolism pathways. Bacterial isolates belonging to genera from the clades, δ-Proteobacteria and γ-Proteobacteria, described previously for their participation in biogeochemical cycling of N-and-S in the OMZs were reported from deoxygenated waters of both the basins. Bacteria involved in anammox such as Candidatus Scalindua were found to be relatively high at ASTS and II2 locations in the Arabian Sea. Further studies are required to ascertain the role of abundant bacteria along the dynamic oceanographic processes in the OMZs.

Contributions of single-cell genomics to our understanding of planktonic marine archaea

Single-cell genomics has transformed many fields of biology, marine microbiology included. Here, we consider the impact of single-cell genomics on a specific group of marine microbes-the planktonic marine archaea. Despite single-cell enabled discoveries of novel metabolic function in the marine thaumarchaea, population-level investigations are hindered by an overall lower than expected recovery of thaumarchaea in single-cell studies. Metagenome-assembled genomes have so far been a more useful method for accessing genome-resolved insights into the Marine Group II euryarchaea. Future progress in the application of single-cell genomics to archaeal biology in the ocean would benefit from more targeted sorting approaches, and a more systematic investigation of potential biases against archaea in single-cell workflows including cell lysis, genome amplification and genome screening. This article is part of a discussion meeting issue 'Single cell ecology'.

Distinct temporal dynamics of planktonic archaeal and bacterial assemblages in the bays of the Yellow Sea

The Yellow Sea features unique characteristics due to strong tides and nutrient-enriched freshwater outflows from China and Korea. The coupling of archaeal and bacterial assemblages associated with environmental factors at two bay areas in the Yellow Sea was investigated. Temporal variations of the archaeal and bacterial assemblages were shown to be greater than the spatial variations based on an analysis of the 16S rRNA gene sequences. Distinct temporal dynamics of both planktonic archaeal and bacterial assemblages was associated with temperature, NO₂^-, and chlorophyll a ([chl-a]) concentrations in the bays of the Yellow Sea. The [chl-a] was the prime predictor of bacterial abundance, and some taxa were clearly correlated with [chl-a]. Bacteroidetes and Alpha-proteobacteria dominated at high [chl-a] stations while Gamma-proteobacteria (esp. SAR86 clade) and Actinobacteria (Candidatus Actinomarina clade) were abundant at low [chl-a] stations. The archaeal abundance was comparable with the bacterial abundance in most of the October samples. Co-dominance of Marine Group II (MGII) and Candidatus Nitrosopumilus suggests that the assimilation of organic nitrogen by MGII could be coupled with nitrification by ammonia-oxidizing archaea. The distinct temporal dynamics of the archaeal and bacterial assemblages might be attributable to the strong tides and the inflow of nutrient-rich freshwater.

Linking shifts in bacterial community with changes in dissolved organic matter pool in a tropical lake

Bacterioplankton communities have a pivotal role in the global carbon cycle. Still the interaction between microbial community and dissolved organic matter (DOM) in freshwater ecosystems remains poorly understood. Here, we report results from a 12-day mesocosm study performed in the epilimnion of a tropical lake, in which inorganic nutrients and allochthonous DOM were supplemented under full light and shading. Although the production of autochthonous DOM triggered by nutrient addition was the dominant driver of changes in bacterial community structure, temporal covariations between DOM optical proxies and bacterial community structure revealed a strong influence of community shifts on DOM fate. Community shifts were coupled to a successional stepwise alteration of the DOM pool, with different fractions being selectively consumed by specific taxa. Typical freshwater clades as Limnohabitans and Sporichthyaceae were associated with consumption of low molecular weight carbon, whereas Gammaproteobacteria and Flavobacteria utilized higher molecular weight carbon, indicating differences in DOM preference among clades. Importantly, Verrucomicrobiaceae were important in the turnover of freshly produced autochthonous DOM, ultimately affecting light availability and dissolved organic carbon concentrations. Our findings suggest that taxonomically defined bacterial assemblages play definite roles when influencing DOM fate, either by changing specific fractions of the DOM pool or by regulating light availability and DOC levels.

The water depth-dependent co-occurrence patterns of marine bacteria in shallow and dynamic Southern Coast, Korea

To investigate the interactions between bacterial species in relation to the biotic and abiotic environmental fluctuations, free-living (FL), nanoparticle-associated (NP), and microparticle-associated (MP) bacterial community compositions (BCCs) were analyzed. A total of 267 samples were collected from July to December 2016 in the dynamic and shallow southern coastal water of Korea. The variations in BCC mostly depended on planktonic size fraction. Network analysis revealed water depth-dependent co-occurrence patterns of coastal bacterial communities. Higher interspecies connectivity was observed within FL bacteria than NP/MP bacteria, suggesting that FL bacteria with a streamlined genome may need other bacterial metabolites for survival, while the NP/MP copiotrophs may have the self-supporting capacity to produce the vital nutrients. The analysis of topological roles of individual OTUs in the network revealed that several groups of metabolically versatile bacteria (the marine Roseobacters, Flavobacteriales, Desulfobacterales, and SAR406 clade) acted as module hubs in different water depth. In conclusion, interspecies interactions dominated in FL bacteria, compared to NP and MP bacteria; modular structures of bacterial communities and keystone species strongly depended on the water depth-derived environmental factors. Furthermore, the multifunctional, versatile FL bacteria could play pivotal roles in dynamic shallow coastal ecosystems.

Archaea dominate oxic subseafloor communities over multimillion-year time scales

Ammonia-oxidizing archaea (AOA) dominate microbial communities throughout oxic subseafloor sediment deposited over millions of years in the North Atlantic Ocean. Rates of nitrification correlated with the abundance of these dominant AOA populations, whose metabolism is characterized by ammonia oxidation, mixotrophic utilization of organic nitrogen, deamination, and the energetically efficient chemolithoautotrophic hydroxypropionate/hydroxybutyrate carbon fixation cycle. These AOA thus have the potential to couple mixotrophic and chemolithoautotrophic metabolism via mixotrophic deamination of organic nitrogen, followed by oxidation of the regenerated ammonia for additional energy to fuel carbon fixation. This metabolic feature likely reduces energy loss and improves AOA fitness under energy-starved, oxic conditions, thereby allowing them to outcompete other taxa for millions of years.

Pressure-Retaining Sampler and High-Pressure Systems to Study Deep-Sea Microbes Under in situ Conditions

The pelagic realm of the dark ocean is characterized by high hydrostatic pressure, low temperature, high-inorganic nutrients, and low organic carbon concentrations. Measurements of metabolic activities of bathypelagic bacteria are often underestimated due to the technological limitations in recovering samples and maintaining them under in situ environmental conditions. Moreover, most of the pressure-retaining samplers, developed by a number of different labs, able to maintain seawater samples at in situ pressure during recovery have remained at the prototype stage, and therefore not available to the scientific community. In this paper, we will describe a ready-to-use pressure-retaining sampler, which can be adapted to use on a CTD-carousel sampler. As well as being able to recover samples under in situ high pressure (up to 60 MPa) we propose a sample processing in equi-pressure mode. Using a piloted pressure generator, we present how to perform sub-sampling and transfer of samples in equi-pressure mode to obtain replicates and perform hyperbaric experiments safely and efficiently (with <2% pressure variability). As proof of concept, we describe a field application (prokaryotic activity measurements and incubation experiment) with samples collected at 3,000m-depth in the Mediterranean Sea. Sampling, sub-sampling, transfer, and incubations were performed under in situ high pressure conditions and compared to those performed following decompression and incubation at atmospheric pressure. Three successive incubations were made for each condition using direct dissolved-oxygen concentration measurements to determine the incubation times. Subsamples were collected at the end of each incubation to monitor the prokaryotic diversity, using 16S-rDNA/rRNA high-throughput sequencing. Our results demonstrated that oxygen consumption by prokaryotes is always higher under in situ conditions than after decompression and incubation at atmospheric pressure. In addition, over time, the variations in the prokaryotic community composition and structure are seen to be driven by the different experimental conditions. Finally, within samples maintained under in situ high pressure conditions, the active (16S rRNA) prokaryotic community was dominated by sequences affiliated with rare families containing piezophilic isolates, such as Oceanospirillaceae or Colwelliaceae. These results demonstrate the biological importance of maintaining in situ conditions during and after sampling in deep-sea environments.

The Eukaryotic Life on Microplastics in Brackish Ecosystems

Microplastics (MP) constitute a widespread contaminant all over the globe. Rivers and wastewater treatment plants (WWTP) transport annually several million tons of MP into freshwaters, estuaries and oceans, where they provide increasing artificial surfaces for microbial colonization. As knowledge on MP-attached communities is insufficient for brackish ecosystems, we conducted exposure experiments in the coastal Baltic Sea, an in-flowing river and a WWTP within the drainage basin. While reporting on prokaryotic and fungal communities from the same set-up previously, we focus here on the entire eukaryotic communities. Using high-throughput 18S rRNA gene sequencing, we analyzed the eukaryotes colonizing on two types of MP, polyethylene and polystyrene, and compared them to the ones in the surrounding water and on a natural surface (wood). More than 500 different taxa across almost all kingdoms of the eukaryotic tree of life were identified on MP, dominated by Alveolata, Metazoa, and Chloroplastida. The eukaryotic community composition on MP was significantly distinct from wood and the surrounding water, with overall lower diversity and the potentially harmful dinoflagellate Pfiesteria being enriched on MP. Co-occurrence networks, which include prokaryotic and eukaryotic taxa, hint at possibilities for dynamic microbial interactions on MP. This first report on total eukaryotic communities on MP in brackish environments highlights the complexity of MP-associated biofilms, potentially leading to altered microbial activities and hence changes in ecosystem functions.

Biodiversity of biological soil crusts from the Polar Regions revealed by metabarcoding

Biological soil crusts (BSCs) are amalgamations of autotrophic, heterotrophic and saprotrophic organisms. In the Polar Regions, these unique communities occupy essential ecological functions such as primary production, nitrogen fixation and ecosystem engineering. Here, we present the first molecular survey of BSCs from the Arctic and Antarctica focused on both eukaryotes and prokaryotes as well as passive and active biodiversity. Considering sequence abundance, Bryophyta is among the most abundant taxa in all analyzed BSCs suggesting that they were in a late successional stage. In terms of algal and cyanobacterial biodiversity, the genera Chloromonas, Coccomyxa, Elliptochloris and Nostoc were identified in all samples regardless of origin confirming their ubiquitous distribution. For the first time, we found the chrysophyte Spumella to be common in polar BSCs as it was present in all analyzed samples. Co-occurrence analysis revealed the presence of sulfur metabolizing microbes indicating that BSCs also play an important role for the sulfur cycle. In general, phototrophs were most abundant within the BSCs but there was also a diverse community of heterotrophs and saprotrophs. Our results show that BSCs are unique microecosystems in polar environments with an unexpectedly high biodiversity.

Quantifying population-specific growth in benthic bacterial communities under low oxygen using H218O

The benthos in estuarine environments often experiences periods of regularly occurring hypoxic and anoxic conditions, dramatically impacting biogeochemical cycles. How oxygen depletion affects the growth of specific uncultivated microbial populations within these diverse benthic communities, however, remains poorly understood. Here, we applied H₂¹⁸O quantitative stable isotope probing (qSIP) in order to quantify the growth of diverse, uncultured bacterial populations in response to low oxygen concentrations in estuarine sediments. Over the course of 7- and 28-day incubations with redox conditions spanning from hypoxia to euxinia (sulfidic), ¹⁸O labeling of bacterial populations exhibited different patterns consistent with micro-aerophilic, anaerobic, facultative anaerobic, and aerotolerant anaerobic growth. ¹⁸O-labeled populations displaying anaerobic growth had a significantly non-random phylogenetic distribution, exhibited by numerous clades currently lacking cultured representatives within the Planctomycetes, Actinobacteria, Latescibacteria, Verrucomicrobia, and Acidobacteria. Genes encoding the beta-subunit of the dissimilatory sulfate reductase (dsrB) became ¹⁸O labeled only during euxinic conditions. Sequencing of these ¹⁸O-labeled dsrB genes showed that Acidobacteria were the dominant group of growing sulfate-reducing bacteria, highlighting their importance for sulfur cycling in estuarine sediments. Our findings provide the first experimental constraints on the redox conditions underlying increased growth in several groups of "microbial dark matter", validating hypotheses put forth by earlier metagenomic studies.

Planktonic Marine Archaea

Archaea are ubiquitous and abundant members of the marine plankton. Once thought of as rare organisms found in exotic extremes of temperature, pressure, or salinity, archaea are now known in nearly every marine environment. Though frequently referred to collectively, the planktonic archaea actually comprise four major phylogenetic groups, each with its own distinct physiology and ecology. Only one group-the marine Thaumarchaeota-has cultivated representatives, making marine archaea an attractive focus point for the latest developments in cultivation-independent molecular methods. Here, we review the ecology, physiology, and biogeochemical impact of the four archaeal groups using recent insights from cultures and large-scale environmental sequencing studies. We highlight key gaps in our knowledge about the ecological roles of marine archaea in carbon flow and food web interactions. We emphasize the incredible uncultivated diversity within each of the four groups, suggesting there is much more to be done.

Specific Effect of Trace Metals on Marine Heterotrophic Microbial Activity and Diversity: Key Role of Iron and Zinc and Hydrocarbon-Degrading Bacteria

Marine microbes are an important control on the biogeochemical cycling of trace metals, but simultaneously, these metals can control the growth of microorganisms and the cycling of major nutrients like C and N. However, studies on the response/limitation of microorganisms to trace metals have traditionally focused on the response of autotrophic phytoplankton to Fe fertilization. Few reports are available on the response of heterotrophic prokaryotes to Fe, and even less to other biogeochemically relevant metals. We performed the first study coupling dark incubations with next generation sequencing to specifically target the functional and phylogenetic response of heterotrophic prokaryotes to Fe enrichment. Furthermore, we also studied their response to Co, Mn, Ni, Zn, Cu (individually and mixed), using surface and deep samples from either coastal or open-ocean waters. Heterotrophic prokaryotic activity was stimulated by Fe in surface open–ocean, as well as in coastal, and deep open-ocean waters (where Zn also stimulated). The most susceptible populations to trace metals additions were uncultured bacteria (e.g., SAR324, SAR406, NS9, and DEV007). Interestingly, hydrocarbon-degrading bacteria (e.g., Thalassolituus, Marinobacter, and Oleibacter) benefited the most from metal addition across all waters (regions/depths) revealing a predominant role in the cycling of metals and organic matter in the ocean.

Active bacterioplankton community response to dissolved 'free' deoxyribonucleic acid (dDNA) in surface coastal marine waters

Seawater contains dissolved 'free' DNA (dDNA) that is part of a larger <0.2 µm pool of DNA (D-DNA) including viruses and uncharacterised bound DNA. Previous studies have shown that bacterioplankton readily degrade dDNA, and culture-based approaches have identified several potential dDNA-utilising taxa. This study characterised the seasonal variation in D-DNA concentrations at Station L4, a coastal marine observatory in the Western English Channel, and linked changes in concentration to cognate physicochemical and biological factors. The impact of dDNA addition on active bacterioplankton communities at Station L4 was then determined using 16S rRNA high-throughput sequencing and RNA Stable Isotope Probing (RNA SIP) with 13C-labelled diatom-derived dDNA. Compared to other major bacterioplankton orders, the Rhodobacterales actively responded to dDNA additions in amended microcosms and RNA SIP identified two Rhodobacterales populations most closely associated with the genera Halocynthiibacter and Sulfitobacter that assimilated the 13C-labelled dDNA. Here we demonstrate that dDNA is a source of dissolved organic carbon for some members of the major bacterioplankton group the Marine Roseobacter Clade. This study enhances our understanding of roles of specific bacterioplankton taxa in dissolved organic matter cycling in coastal waters with potential implications for nitrogen and phosphorus regeneration processes.

Direct Utilization of Organic Nitrogen by Phytoplankton and Its Role in Nitrogen Cycling Within the Southern California Bight

The new production model attempts to quantify the amount of organic material exported from surface waters based on the form of nitrogen (N) being utilized. Dissolved organic N (DON) is rarely assessed during such investigations and even less is understood about the organisms involved in these different transformations within the complex N cycle. Stable isotope probing (SIP) and uptake activity measurements were combined to investigate the dynamics of new and regenerated production during the spring within the Southern California Bight (SCB). We examined the uptake and assimilation of several nitrogenous substrates at several depths to quantify these processes and identify the active communities across all three domains of life that are driving each transformation. Several reoccurring members closely related to the eukaryotic diatom Chaetoceros, dominated assimilation of NO3 - and urea through the water column, and contributed greatly to the overall production. Prokaryotic growth was predominantly carried out through NH4 + assimilation with transitions from Flavobacteria to Rhodobacteraceae and Marine Group II Euryarchaeota to Marine Group I Thaumarchaeota with increasing depth for bacterial and archaeal clades, respectively. Only urea uptake and SIP activity correlated with each other, likely demonstrating that cellular transport and incorporation of urea were coupled. SIP was therefore able to identify the organisms primarily responsible for urea cycling at each depth during this investigation. The role of diatoms within high nutrient areas are well defined but their part in DON cycling in highly stratified regimes is less well understood. Here we demonstrate their ability to efficiently scavenge urea in situ, allowing certain diatoms to outcompete the rest of the community. This diversion of DON away from the trophically inefficient microbial loop directly back into the larger, particle forming populations would alter the current view of microbial food webs. This proposed "phytoplankton shunt" of organic material could potentially enhance the biological pump by mitigating losses due to trophic transfers while increasing DON flux due to ballasting. Our results provide unique biogeochemical and ecological insight into the dynamics and diversity of N cycling and the organisms involved within the surface waters of the SCB.

Linking Uncultivated Microbial Populations and Benthic Carbon Turnover by Using Quantitative Stable Isotope Probing

Little is known about the ecological role of uncultivated microbial populations in carbon turnover in benthic environments. To better understand this, we used quantitative stable isotope probing (qSIP) to quantify the abundance of diverse, specific groups of uncultivated bacteria and archaea involved in autotrophy and heterotrophy in a benthic lacustrine habitat. Our results provide quantitative evidence for active heterotrophic and autotrophic metabolism of several poorly understood microbial groups, thus demonstrating their relevance for carbon turnover in benthic settings. Archaeal ammonia oxidizers were significant drivers of in situ “dark” primary production supporting the growth of heterotrophic bacteria. These findings expand our understanding of the microbial populations within benthic food webs and the role of uncultivated microbes in benthic carbon turnover.

Benthic environments harbor highly diverse and complex microbial communities that control carbon fluxes, but the role of specific uncultivated microbial groups in organic matter turnover is poorly understood. In this study, quantitative DNA stable isotope probing (DNA-qSIP) was used for the first time to link uncultivated populations of bacteria and archaea to carbon turnover in lacustrine surface sediments. After 1-week incubations in the dark with [¹³C]bicarbonate, DNA-qSIP showed that ammonia-oxidizing archaea (AOA) were the dominant active chemolithoautotrophs involved in the production of new organic matter. Natural ¹³C-labeled organic matter was then obtained by incubating sediments in the dark for 2.5 months with [¹³C]bicarbonate, followed by extraction and concentration of high-molecular-weight (HMW) (>50-kDa) organic matter. qSIP showed that the labeled organic matter was turned over within 1 week by 823 microbial populations (operational taxonomic units [OTUs]) affiliated primarily with heterotrophic Proteobacteria, Chloroflexi, Verrucomicrobia, and Bacteroidetes. However, several OTUs affiliated with the candidate microbial taxa Latescibacteria, Omnitrophica, Aminicentantes, Cloacimonates, AC1, Bathyarchaeota, and Woesearchaeota, groups known only from genomic signatures, also contributed to biomass turnover. Of these 823 labeled OTUs, 52% (primarily affiliated with Proteobacteria) also became labeled in 1-week incubations with [¹³C]bicarbonate, indicating that they turned over carbon faster than OTUs that were labeled only in incubations with ¹³C-labeled HMW organic matter. These taxa consisted primarily of uncultivated populations within the Firmicutes, Bacteroidetes, Verrucomicrobia, and Chloroflexi, highlighting their ecological importance. Our study helps define the role of several poorly understood, uncultivated microbial groups in the turnover of benthic carbon derived from “dark” primary production.

IMPORTANCE Little is known about the ecological role of uncultivated microbial populations in carbon turnover in benthic environments. To better understand this, we used quantitative stable isotope probing (qSIP) to quantify the abundance of diverse, specific groups of uncultivated bacteria and archaea involved in autotrophy and heterotrophy in a benthic lacustrine habitat. Our results provide quantitative evidence for active heterotrophic and autotrophic metabolism of several poorly understood microbial groups, thus demonstrating their relevance for carbon turnover in benthic settings. Archaeal ammonia oxidizers were significant drivers of in situ “dark” primary production supporting the growth of heterotrophic bacteria. These findings expand our understanding of the microbial populations within benthic food webs and the role of uncultivated microbes in benthic carbon turnover.

Effects of Ice-Algal Aggregate Export on the Connectivity of Bacterial Communities in the Central Arctic Ocean

In summer 2012, Arctic sea ice declined to a record minimum and, as a consequence of the melting, large amounts of aggregated ice-algae sank to the seafloor at more than 4,000 m depth. In this study, we assessed the composition, turnover and connectivity of bacterial and microbial eukaryotic communities across Arctic habitats from sea ice, algal aggregates and surface waters to the seafloor. Eukaryotic communities were dominated by diatoms, dinoflagellates and other alveolates in all samples, and showed highest richness and diversity in sea-ice habitats (∼400-500 OTUs). Flavobacteriia and Gammaproteobacteria were the predominant bacterial classes across all investigated Arctic habitats. Bacterial community richness and diversity peaked in deep-sea samples (∼1,700 OTUs). Algal aggregate-associated bacterial communities were mainly recruited from the sea-ice community, and were transported to the seafloor with the sinking ice algae. The algal deposits at the seafloor had a unique community structure, with some shared sequences with both the original sea-ice community (22% OTU overlap), as well as with the deep-sea sediment community (17% OTU overlap). We conclude that ice-algal aggregate export does not only affect carbon export from the surface to the seafloor, but may change microbial community composition in central Arctic habitats with potential effects for benthic ecosystem functioning in the future.

Quantitative isotope incorporation reveals substrate partitioning in a coastal microbial community

To quantitatively link microbial identity with biogeochemical function, we carried out 14 simultaneous stable isotope probing experiments with organic and inorganic C and N substrates to measure the isotope incorporation by over one hundred co-occurring eukaryotic and prokaryotic populations in a coastal community. We found that nitrate was the most commonly incorporated substrate, and that light-driven carbon fixation was carried out by some bacterial taxa from the Flavobacteriales and OM60 (NOR5) clade, in addition to photoautotrophic phytoplankton. We found that organisms that incorporated starch, maltose, glucose, lactose and bicarbonate were phylogenetically clustered, suggesting that specific bacterial lineages specialized in the incorporation of these substrates. The data further revealed that coastal microorganisms spanned a range of resource utilization strategies from generalists to specialists and demonstrated a high level of substrate partitioning, with two thirds of taxa exhibiting unique substrate incorporation patterns and the remaining third shared by no more than three OTUs each. Specialists exhibited more extreme incorporation levels (high or low), whereas generalists displayed more intermediate activity levels. These results shed valuable insights into the bottom-up ecological strategies enabling the persistence of high microbial diversity in aquatic ecosystems.

Linking soil biology and chemistry in biological soil crust using isolate exometabolomics

Metagenomic sequencing provides a window into microbial community structure and metabolic potential; however, linking these data to exogenous metabolites that microorganisms process and produce (the exometabolome) remains challenging. Previously, we observed strong exometabolite niche partitioning among bacterial isolates from biological soil crust (biocrust). Here we examine native biocrust to determine if these patterns are reproduced in the environment. Overall, most soil metabolites display the expected relationship (positive or negative correlation) with four dominant bacteria following a wetting event and across biocrust developmental stages. For metabolites that were previously found to be consumed by an isolate, 70% are negatively correlated with the abundance of the isolate’s closest matching environmental relative in situ, whereas for released metabolites, 67% were positively correlated. Our results demonstrate that metabolite profiling, shotgun sequencing and exometabolomics may be successfully integrated to functionally link microbial community structure with environmental chemistry in biocrust.

Metagenomic sequencing provides a window into microbial community structure and metabolic potential. Here, Swenson et al. integrate metabolomics and shotgun sequencing to functionally link microbial community structure with environmental chemistry in biological soil crust (biocrust).

Identifying protist consumers of photosynthetic picoeukaryotes in the surface ocean using stable isotope probing

Photosynthetic picoeukaryotes contribute a significant fraction of primary production in the upper ocean. Micromonas pusilla is an ecologically relevant photosynthetic picoeukaryote, abundantly and widely distributed in marine waters. Grazing by protists may control the abundance of picoeukaryotes such as M. pusilla, but the diversity of the responsible grazers is poorly understood. To identify protists consuming photosynthetic picoeukaryotes in a productive North Pacific Ocean region, we amended seawater with living ¹⁵ N, ¹³ C-labelled M. pusilla cells in a 24-h replicated bottle experiment. DNA stable isotope probing, combined with high-throughput sequencing of V4 hypervariable regions from 18S rRNA gene amplicons (Tag-SIP), identified 19 operational taxonomic units (OTUs) of microbial eukaryotes that consumed M. pusilla. These OTUs were distantly related to cultured taxa within the dinoflagellates, ciliates, stramenopiles (MAST-1C and MAST-3 clades) and Telonema flagellates, thus, far known only from their environmental 18S rRNA gene sequences. Our discovery of eukaryotic prey consumption by MAST cells confirms that their trophic role in marine microbial food webs includes grazing upon picoeukaryotes. Our study provides new experimental evidence directly linking the genetic identity of diverse uncultivated microbial eukaryotes to the consumption of picoeukaryotic phytoplankton in the upper ocean.

Localized high abundance of Marine Group II archaea in the subtropical Pearl River Estuary: implications for their niche adaptation

Marine Group II archaea are widely distributed in global oceans and dominate the total archaeal community within the upper euphotic zone of temperate waters. However, factors controlling the distribution of MGII are poorly delineated and the physiology and ecological functions of these still-uncultured organisms remain elusive. In this study, we investigated the planktonic MGII associated with particles and in free-living forms in the Pearl River Estuary (PRE) over a 10-month period. We detected high abundance of particle-associated MGII in PRE (up to ∼10⁸ 16S rRNA gene copies/l), which was around 10-fold higher than the free-living MGII in the same region, and an order of magnitude higher than previously reported in other marine environments. 10‰ salinity appeared to be a threshold value for these MGII because MGII abundance decreased sharply below it. Above 10‰ salinity, the abundance of MGII on the particles was positively correlated with phototrophs and MGII in the surface water was negatively correlated with irradiance. However, the abundances of those free-living MGII showed positive correlations with salinity and temperature, suggesting the different physiological characteristics between particle-attached and free-living MGIIs. A nearly completely assembled metagenome, MGIIa_P, was recovered using metagenome binning methods. Compared with the other two MGII genomes from surface ocean, MGIIa_P contained higher proportions of glycoside hydrolases, indicating the ability of MGIIa_P to hydrolyse glycosidic bonds in complex sugars in PRE. MGIIa_P is the first assembled MGII metagenome containing a catalase gene, which might be involved in scavenging reactive oxygen species generated by the abundant phototrophs in the eutrophic PRE. Our study presented the widespread and high abundance of MGII in the water columns of PRE, and characterized the determinant abiotic factors affecting their distribution. Their association with heterotrophs, preference for particles and resourceful metabolic traits indicate MGII might play a significant role in metabolising organic matters in the PRE and other temperate estuarine systems.

Spatial variability of marine bacterial and archaeal communities along the particulate matter continuum

Biotic and abiotic particles shape the microspatial architecture that defines the microbial aquatic habitat, being particles highly variable in size and quality along oceanic horizontal and vertical gradients. We analysed the prokaryotic (bacterial and archaeal) diversity and community composition present in six distinct particle size classes ranging from the pico- to the microscale (0.2 to 200 μm). Further, we studied their variations along oceanographic horizontal (from the coast to open oceanic waters) and vertical (from the ocean surface into the meso- and bathypelagic ocean) gradients. In general, prokaryotic community composition was more variable with depth than in the transition from the coast to the open ocean. Comparing the six size-fractions, distinct prokaryotic communities were detected in each size-fraction, and whereas bacteria were more diverse in the larger size-fractions, archaea were more diverse in the smaller size-fractions. Comparison of prokaryotic community composition among particle size-fractions showed that most, but not all, taxonomic groups have a preference for a certain size-fraction sustained with depth. Species sorting, or the presence of diverse ecotypes with distinct size-fraction preferences, may explain why this trend is not conserved in all taxa.

Evaluating Production of Cyclopentyl Tetraethers by Marine Group II Euryarchaeota in the Pearl River Estuary and Coastal South China Sea: Potential Impact on the TEX86 Paleothermometer

TEX₈₆ [TetraEther indeX of glycerol dialkyl glycerol tetraethers (GDGTs) with 86 carbon atoms] has been widely applied to reconstruct (paleo-) sea surface temperature. Marine Group I (MG-I) Thaumarchaeota were thought to be the primary source of GDGTs constituting the TEX₈₆ formula; however, recent research has suggested that Marine Group II (MG-II) Euryarchaeota may also contribute significantly to the GDGT pool in the ocean. Little is known regarding the potential impact of MG-II Euryarchaeota-derived GDGTs on TEX₈₆ values recorded in marine sediments. In this study, we assessed the relationship between distributions of GDGTs and MG-II Euryarchaeota and evaluated its potential effect on the TEX₈₆ proxy. Lipid and DNA analyses were performed on suspended particulate matter and surface sediments collected along a salinity gradient from the lower Pearl River (river water) and its estuary (mixing water) to the coastal South China Sea (SCS, seawater). TEX₈₆-derived temperatures from the water column and surface sediments were significantly correlated and both were lower than satellite-based temperatures. The ring index (RI) values in these environments were higher than predicted from the calculated TEX₈₆-RI correlation, indicating that the GDGT pool in the water column of the PR estuary and coastal SCS comprises relatively more cyclopentane rings, which thereby altered TEX₈₆ values. Furthermore, the abundance of MG-II Euryarchaeota 16S rRNA gene in the mixing water was two to three orders of magnitude higher than those observed in the river or seawater. Significant linear correlations were observed between the gene abundance ratio of MG-II Euryarchaeota to total archaea and the fractional abundance of GDGTs with cyclopentane rings. Collectively, these results suggest that MG-II Euryarchaeota likely produce a large proportion of GDGTs with 1–4 cyclopentane moieties, which may bias TEX₈₆ values in the water column and sediments. As such, valid interpretation of TEX₈₆ values in the sediment record, particularly in coastal oceans, should consider the contribution from MG-II Euryarchaeota.

A new collagenase enzyme of the marine sponge pathogen Pseudoalteromonas agarivorans NW4327 is uniquely linked with a TonB dependent receptor

The primary pathogen of the Great Barrier Reef sponge Rhopaloeides odorabile, recently identified as a novel strain (NW4327) of Pseudoalteromonas agarivorans, produced collagenase which degraded R. odorabile skeletal fibers. We now report the collagenase of P. agarivorans as a metalloprotease which required Ca²⁺ and Zn²⁺ as cofactors. The collagenase was a TonB dependent receptor (TBDR) having a carboxypeptidase regulatory like domain (CRLD) in the N-terminal along with an outer membrane (OM) channel superfamily domain. The genes for TBDR sub-components and collagenase formed one unified entity in the genome of P. agarivorans NW4327. This association of a collagenase with a TBDR distinguished it from all known functional collagenases till date and for the first time, established the enzymatic capability of TBDRs. Predicted TBDR model demonstrated only 15% identity with ferripyoverdin receptor and the CRLD displayed merely 24% identity with carboxypeptidase catalytic chain. Presence of signal peptide, lack of transmembrane helices, absence of N-terminal in the cytoplasmic side, extracellular localization and recovery from the culture supernatant implicated that the TBDR was secreted. Stronger binding of the collagenase with marine sponge type IV collagen than type I collagen, revealed through molecular docking, indicated higher specificity of the enzyme towards type IV collagen.

Bacterial and archaeal communities inhabiting mussels, sediment and water in Indonesian anchialine lakes

Anchialine lakes are a globally rare and unique ecosystem consisting of saline lakes surrounded by land and isolated from the surrounding marine environment. These lakes host a unique flora and fauna including numerous endemic species. Relatively few studies have, however, studied the prokaryote communities present in these lakes and compared them with the surrounding 'open water' marine environment. In the present study, we used a 16S rRNA gene barcoded pyrosequencing approach to examine prokaryote (Bacteria and Archaea) composition in three distinct biotopes (sediment, water and the mussel Brachidontes sp.) inhabiting four habitats, namely, three marine lakes and the surrounding marine environment of Berau, Indonesia. Biotope and habitat proved significant predictors of variation in bacterial and archaeal composition and higher taxon abundance. Most bacterial sequences belonged to OTUs assigned to the Proteobacteria. Compared to sediment and water, mussels had relatively high abundances of the classes Mollicutes and Epsilonproteobacteria. Most archaeal sequences, in turn, belonged to OTUs assigned to the Crenarchaeota with the relative abundance of crenarchaeotes highest in mussel samples. For both Bacteria and Archaea, the main variation in composition was between water samples on the one hand and sediment and mussel samples on the other. Sediment and mussels also shared much more OTUs than either shared with water. Abundant bacterial OTUs in mussels were related to organisms previously obtained from corals, oysters and the deepsea mussel Bathymodiolus manusensis. Abundant archaeal OTUs in mussels, in contrast, were closely related to organisms previously obtained from sediment.

Ubiquity and quantitative significance of bacterioplankton lineages inhabiting the oxygenated hypolimnion of deep freshwater lakes

The oxygenated hypolimnion accounts for a volumetrically significant part of the global freshwater systems. Previous studies have proposed the presence of hypolimnion-specific bacterioplankton lineages that are distinct from those inhabiting the epilimnion. To date, however, no consensus exists regarding their ubiquity and abundance, which is necessary to evaluate their ecological importance. The present study investigated the bacterioplankton community in the oxygenated hypolimnia of 10 deep freshwater lakes. Despite the broad geochemical characteristics of the lakes, 16S rRNA gene sequencing demonstrated that the communities in the oxygenated hypolimnia were distinct from those in the epilimnia and identified several predominant lineages inhabiting multiple lakes. Catalyzed reporter deposition fluorescence in situ hybridization revealed that abundant hypolimnion-specific lineages, CL500-11 (Chloroflexi), CL500-3, CL500-37, CL500-15 (Planctomycetes) and Marine Group I (Thaumarchaeota), together accounted for 1.5-32.9% of all bacterioplankton in the hypolimnion of the lakes. Furthermore, an analysis of single-nucleotide variation in the partial 16S rRNA gene sequence (oligotyping) suggested the presence of different sub-populations between lakes and water layers among the lineages occurring in the entire water layer (for example, acI-B1 and acI-A7). Collectively, these results provide the first comprehensive overview of the bacterioplankton community in the oxygenated hypolimnion of deep freshwater lakes.

Metabolic Roles of Uncultivated Bacterioplankton Lineages in the Northern Gulf of Mexico "Dead Zone"

Marine regions that have seasonal to long-term low dissolved oxygen (DO) concentrations, sometimes called “dead zones,” are increasing in number and severity around the globe with deleterious effects on ecology and economics. One of the largest of these coastal dead zones occurs on the continental shelf of the northern Gulf of Mexico (nGOM), which results from eutrophication-enhanced bacterioplankton respiration and strong seasonal stratification. Previous research in this dead zone revealed the presence of multiple cosmopolitan bacterioplankton lineages that have eluded cultivation, and thus their metabolic roles in this ecosystem remain unknown. We used a coupled shotgun metagenomic and metatranscriptomic approach to determine the metabolic potential of Marine Group II Euryarchaeota, SAR406, and SAR202. We recovered multiple high-quality, nearly complete genomes from all three groups as well as candidate phyla usually associated with anoxic environments—Parcubacteria (OD1) and Peregrinibacteria. Two additional groups with putative assignments to ACD39 and PAUC34f supplement the metabolic contributions by uncultivated taxa. Our results indicate active metabolism in all groups, including prevalent aerobic respiration, with concurrent expression of genes for nitrate reduction in SAR406 and SAR202, and dissimilatory nitrite reduction to ammonia and sulfur reduction by SAR406. We also report a variety of active heterotrophic carbon processing mechanisms, including degradation of complex carbohydrate compounds by SAR406, SAR202, ACD39, and PAUC34f. Together, these data help constrain the metabolic contributions from uncultivated groups in the nGOM during periods of low DO and suggest roles for these organisms in the breakdown of complex organic matter.

Dead zones receive their name primarily from the reduction of eukaryotic macrobiota (demersal fish, shrimp, etc.) that are also key coastal fisheries. Excess nutrients contributed from anthropogenic activity such as fertilizer runoff result in algal blooms and therefore ample new carbon for aerobic microbial metabolism. Combined with strong stratification, microbial respiration reduces oxygen in shelf bottom waters to levels unfit for many animals (termed hypoxia). The nGOM shelf remains one of the largest eutrophication-driven hypoxic zones in the world, yet despite its potential as a model study system, the microbial metabolisms underlying and resulting from this phenomenon—many of which occur in bacterioplankton from poorly understood lineages—have received only preliminary study. Our work details the metabolic potential and gene expression activity for uncultivated lineages across several low DO sites in the nGOM, improving our understanding of the active biogeochemical cycling mediated by these “microbial dark matter” taxa during hypoxia.