The deep ocean methanosphere is defined by the microbial communities that cycle methane, the animals that directly consume or form symbioses with methane-consuming microbes, and the transitional animal communities that gain energy indirectly from methane and/or take advantage of the methane-derived authigenic carbonate. Our research seeks to redefine our understanding of the fate and footprint of methane on Pacific continental margins. By applying molecular, isotopic, geochemical, and radiotracer tools to the seep microbes and fauna we hope to better understand the contribution of methane to deep-sea diversity and ecosystem function. During the 2023 expedition AT50-12 with the RV Atlantis and the submersible Alvin we explored a set of methane seeps located in the Southern California Borderland. Samples were taken from seep carbonates, sediments, and the water column surrounding methane vents to study microbial methanotrophic activity and its relevance for methane removal, habitat engineering, and primary productivity. This poster will provide a first glance into new datasets on methanotrophy generated during the expedition and into the heterogeneity of deep ocean methane seeps off the coast of southern California.

Dense microbial communities, like the gut and soil microbiomes, are dynamic societies. Bacteria can navigate these environments by deploying proteins (effectors) that alter foreign cells’ behavior. Immunity proteins preferentially protect neighboring sibling cells, in contrast to canonical toxin-antitoxin systems. A prevailing hypothesis is that when immunity proteins are bound to specific (cognate) protein partners, it is sufficient to disrupt their function; further, there is little-to-no crosstalk with other (non-cognate) effectors. Here, we build on sporadic reports challenging these hypotheses. We show that immunity proteins from a newly defined protein family can bind and protect against non-cognate PD-(D/E)XK-containing effectors from diverse phyla. We describe the domains essential for binding and function and show that binding alone is insufficient for protective activity. Moreover, we found that these effector and immunity genes co-occur in individual human microbiomes. These results expand the growing repertoire of bacterial protection mechanisms and force us to reconsider how non-cognate interactions impact community structure within complex ecosystems.

Investigations of the metabolic capabilities of anaerobic protists advances our understanding of the evolution of eukaryotic life on Earth and for uncovering analogous extraterrestrial complex microbial life. Certain species of foraminiferan protists live in environments analogous to early Earth conditions when eukaryotes evolved, including sulfidic, anoxic and hypoxic sediment porewaters. Foraminifera are known to form symbioses as well as to harbor organelles from other eukaryotes (chloroplasts), possibly bolstering the host's independence from oxygen. The full extent of foraminiferal physiological capabilities is not fully understood. To date, evidence for foraminiferal anaerobiosis was gleaned from specimens first subjected to stresses associated with removal from in situ conditions. Here, we report comprehensive gene expression analysis of benthic foraminiferal populations preserved in situ on the euxinic (anoxic and sulfidic) bathyal seafloor, thus avoiding environmental alterations associated with sample recovery, including pressure reduction, sunlight exposure, warming, and oxygenation. Metatranscriptomics, metagenome-assembled genomes, and measurements of substrate uptake were used to study the kleptoplastidic foraminifer Nonionella stella inhabiting sulfur-oxidizing bacterial mats of the Santa Barbara Basin, off California. We show N. stella energy generation under dark euxinia is unusual because it orchestrates complex metabolic pathways for ATP production and carbon fixation through the Calvin cycle. These pathways include extended glycolysis, anaerobic fermentation, sulfide oxidation, and the presence of a membrane-bound inorganic pyrophosphatase, an enzyme that hydrolyzes inorganic pyrophosphate to actively pump protons across the mitochondrial membrane.

Despite their large environmental impact and multiple independent emergences, the processes leading to the evolution of anaerobic methanotrophic archaea (ANME) remain unclear. This work uses comparative metagenomics of a recently evolved but understudied ANME group, ‘ Candidatus Methanovorans’ (ANME-3) to identify evolutionary processes and innovations at work in ANME which may be obscured in earlier evolved lineages. Within members of Methanovorans , we identified convergent evolution in carbon and energy metabolic genes as likely drivers of ANME evolution. We also identified erosion of genes required for methylotrophic methanogenesis along with horizontal acquisition of multi-heme cytochromes and other loci uniquely associated with ANME. The assembly and comparative analysis of multiple Methanovorans genomes offers important functional context for understanding the niche-defining metabolic differences between methane-oxidizing ANME and their methanogen relatives. Furthermore, this work illustrates the multiple evolutionary modes at play in the transition to a novel and globally important metabolic niche.### Competing Interest StatementThe authors have declared no competing interest.

Scientists studying deep ocean microbial ecosystems use limited numbers of sediment samples collected from the seafloor to characterize important life-sustaining biogeochemical cycles in the environment. Yet conducting fieldwork to sample these extreme remote environments is both expensive and time consuming, requiring tools that enable scientists to explore the sampling history of field sites and predict where taking new samples is likely to maximize scientific return. We conducted a collaborative, user-centered design study with a team of scientific researchers to develop DeepSee, an interactive data workspace that visualizes 2D and 3D interpolations of biogeochemical and microbial processes in context together with sediment sampling history overlaid on 2D seafloor maps. Based on a field deployment and qualitative interviews, we found that DeepSee increased the scientific return from limited sample sizes, catalyzed new research workflows, reduced long-term costs of sharing data, and supported teamwork and communication between team members with diverse research goals.

The human oral and nasal cavities can act as reservoirs for opportunistic pathogens capable of causing acute infection. These microbes asymptomatically colonize the human oral and nasal cavities which facilitates transmission within human populations via the environment, and they routinely possess clinically significant antibiotic resistance genes. Among these opportunistic pathogens, the Klebsiella genus stands out as a notable example, with its members frequently linked to nosocomial infections and multidrug resistance. As with many colonizing opportunistic pathogens, the essential transmission factors influencing the spread of Klebsiella species among both healthy and diseased individuals remain unclear. Here, we explored a possible explanation by investigating the ability of oral and nasal Klebsiella species to outcompete their native microbial community members under in vitro starvation conditions, which could be analogous to external hospital environments or the microenvironment of mechanical ventilators. When K. pneumoniae and K. aerogenes were present within a healthy human oral or nasal sample, the bacterial community composition shifted dramatically under starvation conditions and typically became enriched in Klebsiella species. Furthermore, introducing K. pneumoniae exogenously into a native microbial community lacking K. pneumoniae, even at low inoculum, led to repeated enrichment under starvation. Precise monitoring of K. pneumoniae within these communities undergoing starvation indicated rapid initial growth and prolonged viability compared to other members of the microbiome. K. pneumoniae strains isolated from healthy individuals’ oral and nasal cavities also exhibited resistance to multiple classes of antibiotics and were genetically similar to clinical and gut isolates. In addition, we found that in the absence of Klebsiella species, other understudied opportunistic pathogens, such as Peptostreptococcus, increased in relative abundance under starvation conditions. Our findings establish an environmental and microbiome community circumstance that allows for the enrichment of Klebsiella species and other opportunistic pathogens. Klebsiella’s enrichment may hinge on its ability to quickly outgrow other members of the microbiome. The ability to outcompete other commensal bacteria and to persist under harsh environmental conditions could be an important factor that contributes to enhanced transmission in both commensal and pathogenic contexts.

Discovering new deep hydrothermal vent systems is one of the biggest challenges in ocean exploration. They are a unique window to elucidate the physical, geochemical, and biological processes that occur on the seafloor and are involved in the evolution of life on Earth. In this study, we present a molecular analysis of the microbial composition within the newly discovered hydrothermal vent field, JaichMaa ‘ja ‘ag, situated in the Southern Pescadero Basin within the Gulf of California. During the cruise expedition FK181031 in 2018, 33 sediment cores were collected from various sites within the Pescadero vent fields and processed for 16S rRNA amplicon sequence variants (ASVs) and geochemical analysis. Correlative analysis of the chemical composition of hydrothermal pore fluids and microbial abundances identified several sediment-associated phyla, including Thermotogota, that appear to be enriched in sediment horizons impacted by hydrothermal fluid flow. Comparative analysis of Thermotogota with the previously explored Auka hydrothermal vent field situated 2 km away displayed broad similarity between the two locations, although at finer scales (e.g., ASV level), there were notable differences that point to core-to-core and site-level factors revealing distinct patterns of distribution and abundance within these two sediment-hosted hydrothermal vent fields. These patterns are intricately linked to the specific physical and geochemical conditions defining each vent, illuminating the complexity of this unique deep ocean chemosynthetic ecosystem.

Despite being typically perceived as "clonal" organisms, bacteria and archaea possess numerous mechanisms to share and co-opt genetic material from other lineages. Several mechanisms for horizontal gene transfer have been discovered, but the high mosaicity observed in many bacterial genomes outscales that explained by known mechanisms, hinting at yet undiscovered processes. In this issue of Cell, Hackl et al. introduce a new category of mobile genetic elements called tycheposons, providing a novel mechanism that contributes to the prodigious genomic diversity within microbial populations. The discovery and characterization of tycheposons prompts a reevaluation of microbial diversification in complex environments.

Certain benthic foraminifera thrive in marine sediments with low or undetectable oxygen. Potential survival avenues used by these supposedly aerobic protists include fermentation and anaerobic respiration, although details on their adaptive mechanisms remain elusive. To better understand the metabolic versatility of foraminifera, we studied two benthic species that thrive in oxygen-depleted marine sediments. Here we detail, via transcriptomics and metatranscriptomics, differential gene expression of Nonionella stella and Bolivina argentea , collected from Santa Barbara Basin, California, USA, in response to varied oxygenation and chemical amendments. Organelle-specific metabolic reconstructions revealed these two species utilize adaptable mitochondrial and peroxisomal metabolism. N. stella , most abundant in anoxia and characterized by lack of food vacuoles and abundance of intracellular lipid droplets, was predicted to couple the putative peroxisomal beta-oxidation and glyoxylate cycle with a versatile electron transport system and a partial TCA cycle. In contrast, B. argentea , most abundant in hypoxia and contains food vacuoles, was predicted to utilize the putative peroxisomal gluconeogenesis and a full TCA cycle but lacks the expression of key beta-oxidation and glyoxylate cycle genes. These metabolic adaptations likely confer ecological success while encountering deoxygenation and expand our understanding of metabolic modifications and interactions between mitochondria and peroxisomes in protists.

The oral microbiome represents a microbial community of critical relevance to human health. Recent studies have documented the diversity and dynamics of different bacteria to reveal a rich, stable ecosystem characterized by strain-level dynamics.

Here, we report draft genome sequences for nine strains of “ Candidatus Nanosynbacter sp. HMT-352.” These strains and their sequences were used to interrogate strain-level variations in host range, gene content, and growth dynamics among the phylum “ Candidatus Saccharibacteria.”

Background: There have been only a few brain computed tomography imaging studies, with mostly negative findings, in subjects with borderline personality disorder (BPD). This is the first MRI study which evaluated the structural abnormalities of the brain in subjects with the sole diagnosis of BPD. Methods: Twenty-five subjects with BPD were compared with age-, gender-matched healthy comparison subjects (n=25) on volumes of the frontal lobes, the temporal lobes, the lateral ventricles, and the cerebral hemispheres in brain magnetic resonance imaging. Results: Subjects with BPD had a significantly smaller frontal lobe compared to comparison subjects (multivariate regression analysis, t=2.225, df=46, P=0.031). There were no significant differences in volumes of the temporal lobes, the lateral ventricles, and the cerebral hemispheres between subjects with and without BPD. Limitations: Strict inclusion and exclusion criteria employed in the present study may make it difficult to generalize our findings. The gray matter and white matter of the brain were not measured separately. Differences in head tilt during image acquisition were not corrected. Conclusions: The current study reports a smaller frontal lobe volume on brain MRI in subjects with BPD compared with healthy comparison subjects. This finding may serve as a potentially useful biological variable that may allow for subtyping BPD.

The evidence for the presence of a diverse and abundant phage population in the host-associated oral microbiome came largely from metagenomic analysis or the observation of virus-like particles within saliva/plaque samples, while the isolation of oral phage and investigation of their interaction with bacterial hosts are limited. Here, we report the isolation of LC001, the first lytic phage targeting oral Schaalia odontolytica .

Saccharibacteria (TM7), which are obligate episymbionts growing on the surface of host bacteria, may play an important role in oral disease, such as periodontitis (1, 2). As TM7 is a newly cultured lineage of bacteria, its research is limited by the small number of isolated representatives relative to the number of TM7 genomes assembled from culture-independent studies (3-5). A comprehensive view of both TM7 taxa and TM7 strain-level variations remains opaque. In this study, we expanded our previously developed TM7 baiting method into using many host bacteria in parallel, which allowed us to obtain 37 TM7 strains from the human oral cavity. These strains were further classified into low-enrichment (LE, n = 24) and high-enrichment (HE, n = 13) groups based on their proficiency at propagating on host bacteria. Of the 13 HE strains, 10 belong to "Candidatus Nanosynbacter sp." strain HMT-352 (human microbial taxon) (6), enabling us to explore both the phenotypic and genomic strain variations within a single TM7 species. We show that TM7 HMT-352 strains exhibit a diverse host range and varied growth dynamics during the establishment of their episymbiotic relationship with host bacteria. Furthermore, despite HMT-352 strains sharing a majority of their genes, we identified several gene clusters that may play a pivotal role in host affinity. More importantly, our comparative analyses also provide TM7 gene candidates associated with strain-level phenotypic variation that may be important for episymbiotic interactions with host bacteria. IMPORTANCE Candidate phylum radiation (CPR) bacteria comprise a poorly understood phylum that is estimated to encompass similar to 26% of all diversity of domain bacteria. Among CPR bacteria, the Saccharibacteria lineage (TM7) is of particular interest, as it is found in high abundance in the mammal microbiome and has been associated with oral disease. While many CPR genomes, TM7 included, have been acquired through culture-independent methods, only a small number of representatives have been isolated. Such isolated representatives, however, shed light on the physiology, pathogenesis, and episymbiotic interactions of TM7. Combined with genomic analyses, experiments involving isolated representatives can distinguish phylogenetic to phenotypic discrepancies and better identify genes of importance. In this study, we utilized multiple host bacteria in parallel to isolate TM7 bacteria and examined strain-level variation in TM7 to reveal key genes that may drive TM7-host interactions. Our findings accentuate that broad phylogenetic characterization of CPR is the next step in understanding these bacteria.

Saccharibacteria (TM7) are obligate epibionts living on the surface of their host bacteria and are strongly correlated with dysbiotic microbiomes during periodontitis and other inflammatory diseases, suggesting they are putative pathogens. However, due to the recalcitrance of TM7 cultivation, causal research to investigate their role in inflammatory diseases is lacking. Here, we isolated multiple TM7 species on their host bacteria from periodontitis patients. These TM7 species reduce inflammation and consequential bone loss by modulating host bacterial pathogenicity in a mouse ligature-induced periodontitis model. Two host bacterial functions involved in collagen binding and utilization of eukaryotic sialic acid are required for inducing bone loss and are altered by TM7 association. This TM7-mediated downregulation of host bacterial pathogenicity is shown for multiple TM7/host bacteria pairs, suggesting that, in contrast to their suspected pathogenic role, TM7 could protect mammalian hosts from inflammatory damage induced by their host bacteria.

Oceanic deoxygenation is increasingly affecting marine ecosystems; many taxa will be severely challenged, yet certain nominally aerobic foraminifera (rhizarian protists) thrive in oxygen-depleted to anoxic, sometimes sulfidic, sediments uninhabitable to most eukaryotes. Gene expression analyses of foraminifera common to severely hypoxic or anoxic sediments identified metabolic strategies used by this abundant taxon. In field-collected and laboratory-incubated samples, foraminifera expressed denitrification genes regardless of oxygen regime with a putative nitric oxide dismutase, a characteristic enzyme of oxygenic denitrification. A pyruvate:ferredoxin oxidoreductase was highly expressed, indicating the capability for anaerobic energy generation during exposure to hypoxia and anoxia. Near-complete expression of a diatom's plastid genome in one foraminiferal species suggests kleptoplasty or sequestration of functional plastids, conferring a metabolic advantage despite the host living far below the euphotic zone. Through a unique integration of functions largely unrecognized among "typical" eukaryotes, benthic foraminifera represent winning microeukaryotes in the face of ongoing oceanic deoxygenation.

Background The increasing availability of microbial genomes and environmental shotgun metagenomes provides unprecedented access to the genomic differences within related bacteria. The human oral microbiome with its diverse habitats and abundant, relatively well-characterized microbial inhabitants presents an opportunity to investigate bacterial population structures at an ecosystem scale. Results Here, we employ a metapangenomic approach that combines public genomes with Human Microbiome Project (HMP) metagenomes to study the diversity of microbial residents of three oral habitats: tongue dorsum, buccal mucosa, and supragingival plaque. For two exemplar taxa, Haemophilus parainfluenzae and the genus Rothia, metapangenomes reveal distinct genomic groups based on shared genome content. H. parainfluenzae genomes separate into three distinct subgroups with differential abundance between oral habitats. Functional enrichment analyses identify an operon encoding oxaloacetate decarboxylase as diagnostic for the tongue-abundant subgroup. For the genus Rothia, grouping by shared genome content recapitulates species-level taxonomy and habitat preferences. However, while most R. mucilaginosa are restricted to the tongue as expected, two genomes represent a cryptic population of R. mucilaginosa in many buccal mucosa samples. For both H. parainfluenzae and the genus Rothia, we identify not only limitations in the ability of cultivated organisms to represent populations in their native environment, but also specifically which cultivar gene sequences are absent or ubiquitous. Conclusions Our findings provide insights into population structure and biogeography in the mouth and form specific hypotheses about habitat adaptation. These results illustrate the power of combining metagenomes and pangenomes to investigate the ecology and evolution of bacteria across analytical scales.

Host range is a fundamental component of symbiotic interactions, yet it remains poorly characterized for the prevalent yet enigmatic subcategory of bacteria/bacteria symbioses. The recently characterized obligate bacterial epibiont Candidatus Nanosynbacter lyticus TM7x with its bacterial host Actinomyces odontolyticus XH001 offers an ideal system to study such a novel relationship. In this study, the host range of TM7x was investigated by coculturing TM7x with various related Actinomyces strains and characterizing their growth dynamics from initial infection through subsequent co-passages. Of the twenty-seven tested Actinomyces , thirteen strains, including XH001, could host TM7x, and further classified into “permissive” and “nonpermissive” based on their varying initial responses to TM7x. Ten permissive strains exhibited growth/crash/recovery phases following TM7x infection, with crash timing and extent dependent on initial TM7x dosage. Meanwhile, three nonpermissive strains hosted TM7x without a growth-crash phase despite high TM7x dosage. The physical association of TM7x with all hosts, including nonpermissive strains, was confirmed by microscopy. Comparative genomic analyses revealed distinguishing genomic features between permissive and nonpermissive hosts. Our results expand the concept of host range beyond a binary to a wider spectrum, and the varying susceptibility of Actinomyces strains to TM7x underscores how small genetic differences between hosts can underly divergent selective trajectories.

In mixed-species communities, bacteria can deploy contact-dependent effectors to compete with other organisms, often directly injecting these proteins into neighboring cells. One current hypothesis is that the entire protein contains information specific for a single species; emergence of new effectors comes from acquiring genes. Here we have characterized a family of DNA-degrading effectors that are nucleases which cause death. Like other families of chimeric nucleases, these effectors contain two domains. One is a PD-(D/E)XK-containing domain necessary for DNA cleavage. The other domain, which does not contain known DNA-binding structures, encodes species-identifying information. We capitalized on the species-identifying domain to differentiate among low-abundance species, as well as to reveal domain architectures within these proteins, in human gut and oral microbiomes. Emerging are questions about how low-abundance strains use effectors for survival and how strain-identifying effectors evolve. ![Figure][1] [1]: pending:yes