Biology subjects

Breusing, C.

Publications and source records attributed to Breusing, C..

11 recordsLinked to original sources

bioRxiv2026

Seafloor topography structures subseafloor microbial communities in the Puerto Rico Trench

The influence of seafloor topography on subseafloor microbial communities is poorly understood. In this study, we systematically sampled subseafloor sedimentary microbial communities and pore-water geochemistry at bathyal, abyssal, and hadal water depths of the Puerto Rico Trench. The Puerto Rico Trench exhibits vertical relief of over 8 km with seafloor topography shaped by active plate tectonics and characterized by a very steep southern wall and active mass wasting. Sampling across these features, we find that subseafloor microbial communities are influenced by topography in the following two ways. First, subseafloor sediment in the deepest part of the trench is anoxic, enriched in organic matter due to mass transport of sediment from shallower water depths, and contains an anaerobic subseafloor community that is quite distinct from the anaerobic subseafloor community in anoxic sediment at bathyal depths. The difference between these bathyal and hadal subseafloor anaerobic communities is consistent with influence of water-depth-related physical properties on subseafloor community composition. Second, subseafloor sediment remains oxygenated for meters below seafloor on steep slopes within the bathyal zone, an abyssal topographic high within the trench, and the abyssal plain seaward of the trench subseafloor, likely due to limited sediment accumulation, which selects for the presence of aerobic microbial communities. The difference between these bathyal and abyssal aerobic subseafloor communities and the anaerobic communities at bathyal and hadal depths reflects the role of seafloor topography in structuring subseafloor availability of redox reactants, which in turn drives the activities and composition of subseafloor microbial communities.

microbiology↗

bioRxiv2026

Convergent and divergent patterns of holobiont evolution in co-distributed chemosynthetic symbioses

Intraspecific variation in microbial symbioses is shaped by a variety of ecological and evolutionary processes. In geographically separated populations, divergence in genomic traits is expected due to dispersal barriers and habitat differentiation, whereas sympatric populations might exhibit functional convergence to the characteristics of a shared environment. While these two processes have been well documented in many animal and plant species, they remain understudied in symbiotic systems. Here, we examined these processes in Atlantic cold seep mussel species that associate with environmentally acquired methane and/or sulfur-oxidizing bacteria. Using genomic methods, we reveal an eco-geographical barrier between the Western Atlantic and Gulf of Mexico that influences the distribution of symbiont species and the level of divergence between holobiont populations. While host populations were only slightly differentiated across this divide, symbiont populations were structured both between and within regions. The sulfur-oxidizing symbionts contained different regional types of dissimilatory nitrate reductase, possibly due to variation in oxygen availability. The methane-oxidizing symbionts showed evidence for convergent evolution, such as retention of a secondary, iron-dependent methane monooxygenase in Western Atlantic populations, driven by local copper limitation. These findings advance our understanding of divergent and convergent adaptive mechanisms underlying intraspecific host-symbiont variation in horizontally transmitted symbioses.

evolutionary biology↗

bioRxiv2026

Piezophilic activity dominates the Puerto Rico Trench deep subseafloor biosphere

Hydrostatic pressure is a defining feature of the deep ocean, yet how it structures microbial activity across the subseafloor biosphere is poorly understood. Here, we assess pressure effects on anabolic activity in seafloor and subseafloor communities across a margin-to-hadal-to-abyssal transect of the Puerto Rico Trench region (493-8,385 m water depth). Community-level responses to pressure reverse with burial, revealing a previously unrecognized shift toward piezophily in resident subseafloor communities down to 20 meters below seafloor (mbsf). In pressure-incubation experiments, atmospheric pressure yielded higher proportions of active cells in surficial sediments, whereas in situ pressure yielded higher proportions in the subseafloor. Pressure also structured active-community composition; in trench-axis sediments extending to 8.35 mbsf, JS1/Atribacterota populations belonging to geographically widespread hadal lineages exhibited a physiological response to in situ pressure, indicative of subseafloor piezophily. These findings suggest that hydrostatic pressure acts as an ecological filter after burial, favoring piezophilic traits that may support microbial persistence in the deep subseafloor biosphere.

microbiology↗

bioRxiv2025

Population genomic insights into syntrophic symbioses between marine anaerobic ciliates and intracellular methanogens

Symbiotic interactions are an ecologically and evolutionary significant phenomenon pertaining to virtually every organism on Earth. For eukaryotes inhabiting extreme environments, syntrophic symbioses with microbes may be key to successfully colonizing new niches, such as globally expanding oxygen-depleted habitats. Multi-domain symbioses between microbial eukaryotes and intracellular methanogenic archaea are crucial to understanding the origins and mechanisms of eukaryotic anaerobiosis. Nearly all anaerobic ciliates, ecologically important protists found in diverse oxygen-depleted environments, host methanogenic endosymbionts, sometimes alongside bacterial partners, that facilitate their anaerobic metabolism. Although vertical symbiont transmission necessarily occurs during ciliate cell division, symbionts might occasionally be acquired horizontally. However, patterns of host-symbiont specificity and intraspecific variability remain poorly understood. Here, we present the first intra-specific genomic analysis of both host and symbionts in such partnerships, providing key insights into the fidelity of eukaryotic-prokaryotic liaisons in anoxia. We assessed the symbiont-host co-diversification and genetic variation across eleven populations of a single undescribed Metopus species hosting Methanocorpusculum cultured from intertidal sediment locations separated by meters to 1000s of kilometers. Our results show incongruency in host mitochondrial and symbiont phylogenies, indicating a mixed transmission mode. On a genomic level, both host and symbiont populations formed distinct location-specific clusters exhibiting no signs of isolation-by-distance. Instead, ecological factors appear to have driven population genomic divergence at least partly and likely led to differences in metabolic traits. Symbiont comparative and population genomics enable us to further comprehend the complex nature of these multi-partner syntrophic symbioses, crucial to interpreting cell-cell interactions across the domains of life.

microbiology↗

bioRxiv2025

Contrasting genomic responses of hydrothermal vent animals and their symbionts to population decline after the Hunga volcanic eruption

Genetic bottlenecks are evolutionary events that reduce the effective size and diversity of natural populations, often limiting a populations ability to adapt to environmental change. Given the accelerating human impact on ecosystems worldwide, understanding how populations evolve after a genetic bottleneck is becoming increasingly important for species conservation. Ash deposits from the 2022 Hunga volcanic eruption in the Southwest Pacific led to a drastic decline of animal symbioses associated with hydrothermal vents in this region, allowing insights into the effects of population bottlenecks in the deep sea. Here, we applied metagenomic sequencing to pre- and post-eruption samples of mollusk-microbial symbioses from the Lau Basin to investigate patterns of genetic variation and effective population size. Our data indicate that animal host populations currently show only small changes in genome-wide diversity but in most cases experienced a long-term decline in effective size that was likely intensified by the volcanic impact. By contrast, symbiont populations exhibited a notable decrease in genomic variation, including loss of certain habitat-specific strains. However, detection of environmental symbiont sequences suggests that lost strain diversity might be recovered from the free-living symbiont pool. The differences between host and symbiont populations might be related to their contrasting genetic structures and levels of gene flow, although the full extent of population bottlenecks in the host animals might only be recognizable after a few generations. These results add to our understanding of the evolutionary dynamics of animal-microbe populations following a natural disturbance and help assess their resilience to potential future anthropogenic impacts.

evolutionary biology↗

bioRxiv2022

Host mixotrophy, habitat stability and recombination may all decrease geographic differentiation between symbiont populations in Western Pacific deep-sea mussels

The intra-host composition of horizontally transmitted microbial symbionts can vary across host populations due to interactive effects of host genetics, environmental and geographic factors. While adaptation to local habitat conditions can drive geographic subdivision of symbiont strains, it is unknown whether these patterns are universal and how differences in ecological characteristics among host-symbiont associations influence the genomic structure of symbiont populations. To address this question, we sequenced metagenomes of different populations of the deep-sea mussel Bathymodiolus septemdierum, which are common at Western Pacific deep-sea hydrothermal vents and show characteristic patterns of niche partitioning with sympatric gastropod symbioses. Bathymodiolus septemdierum lives in close symbiotic relationship with sulfur-oxidizing chemosynthetic bacteria but supplements its symbiotrophic diet through filter-feeding, enabling it to occupy ecological niches with less exposure to geochemical reductants. Our analyses indicate that symbiont populations associated with B. septemdierum show structuring by geographic location, but that the dominant symbiont strain is uncorrelated with vent site. These patterns are in contrast to co-occurring Alviniconcha and Ifremeria symbioses that exhibit greater symbiont nutritional dependence and occupy habitats with higher spatial variability in environmental conditions. Our results suggest that relative habitat homogeneity combined with sufficient symbiont dispersal and genomic mixing might promote persistence of similar symbiont strains across geographic locations, while mixotrophy might decrease selective pressures on the host to affiliate with locally adapted symbiont strains. Overall, these data contribute to our understanding of the potential mechanisms influencing symbiont population structure across a spectrum of marine microbial symbioses that vary in ecological niche and relative host dependency.

evolutionary biology↗

bioRxiv2022

Geography, not lifestyle, explains the population structure of free-living and host-associated deep-sea hydrothermal vent snail symbionts

Marine symbioses are predominantly established through horizontal acquisition of microbial symbionts from the environment. However, genetic and functional comparisons of free-living populations of symbionts to their host-associated counterparts are sparse. Here, we assembled the first genomes of the chemoautotrophic gammaproteobacterial symbionts affiliated with the deep-sea snail Alviniconcha hessleri from two separate hydrothermal vent fields of the Mariana Back-Arc Basin. We used phylogenomic and population genomic methods to assess sequence and gene content variation between free-living and host-associated symbionts. Our phylogenomic analyses show that the free-living and host-associated symbionts of A. hessleri from both vent fields are populations of monophyletic strains from a single species. Furthermore, genetic structure and gene content analyses indicate that these symbiont populations are differentiated by vent field rather than by lifestyle. Together, this work suggests that, despite the potential influence of host-mediated acquisition and release processes on horizontally transmitted symbionts, geographic isolation and/or adaptation to local habitat conditions are important determinants of symbiont population structure and intra-host composition.

microbiology↗

bioRxiv2021

Host-symbiont population genomics provide insights into partner fidelity, transmission mode and habitat adaptation in deep-sea hydrothermal vent snails

Symbiont specificity, both at the phylotype and strain level, can have profound consequences for host ecology and evolution. However, except for insights from a few model symbiosis systems, the degree of partner fidelity and the influence of host versus environmental factors on symbiont composition are still poorly understood. Nutritional symbioses between invertebrate animals and chemosynthetic bacteria at deep-sea hydrothermal vents are examples of relatively selective associations, where hosts affiliate only with particular, environmentally acquired phylotypes of gammaproteobacterial or campylobacterial symbionts. In hydrothermal vent snails of the sister genera Alviniconcha and Ifremeria this phylotype specificity has been shown to play a role in habitat distribution and partitioning among different holobiont species. However, it is currently unknown if fidelity goes beyond species level associations that might influence genetic structuring, connectivity and habitat adaptation of holobiont populations. We used metagenomic analyses to assess sequence variation in hosts and symbionts and identify correlations with geographic and environmental factors. Our analyses indicate that host populations are not differentiated across a ~800 km gradient, while symbiont populations are clearly structured between vent locations due to a combination of neutral and selective processes. Overall, these results suggest that host individuals flexibly associate with locally adapted strains of their specific symbiont phylotypes, which supports a long-standing but untested paradigm of the benefits of horizontal transmission. Strain flexibility in these snails likely enables host populations to exploit a range of habitat conditions, which might favor wide-spread genetic connectivity and ecological resilience unless physical dispersal barriers are present. Significance StatementSymbiont composition in horizontally transmitted symbioses is influenced by a combination of host genetics, environmental conditions and geographic barriers. Yet the relative importance of these factors and the effects of adaptive versus neutral evolutionary forces on symbiont population structure remain unknown in the majority of marine symbioses. To address these questions, we applied population genomic approaches in four species of deep-sea hydrothermal vent snails that live in obligate association with chemosynthetic bacteria. Our analyses show that host genetics plays a minor role compared to environment for symbiont strain composition despite specificity to symbiont species and corroborate a long-standing hypothesis that vent invertebrates affiliate with locally adapted symbiont strains to cope with the variable habitat conditions characterizing hydrothermal vents.

molecular biology↗

bioRxiv2020

Differences in cofactor, oxygen and sulfur requirements influence niche adaptation in deep-sea vesicomyid clam symbioses

Vertical transmission of bacterial endosymbionts is accompanied by virtually irreversible gene loss that can provide insights into adaptation to divergent ecological niches. While patterns of genome reduction have been well described in some terrestrial symbioses, they are less understood in marine systems where vertical transmission is relatively rare. The association between deep-sea vesicomyid clams and chemosynthetic Gammaproteobacteria is one example of maternally inherited symbioses in the ocean. Differences in nitrogen and sulfur physiology between the two dominant symbiont groups, Ca. Ruthia and Ca. Vesicomyosocius, have been hypothesized to influence niche exploitation, which likely affects gene content evolution in these symbionts. However, genomic data are currently limited to confirm this assumption. In the present study we sequenced and compared 11 vesicomyid symbiont genomes with existing assemblies for Ca. Vesicomyosocius okutanii and Ca. Ruthia magnifica. Our analyses indicate that the two vesicomyid symbiont groups have a common core genome related to chemosynthetic metabolism, but differ in their potential for nitrate respiration and flexibility to environmental sulfide concentrations. Moreover, Ca. Vesicomyosocius and Ca. Ruthia have different enzymatic requirements for cobalamin and nickel and show contrasting capacities to acquire foreign genetic material. Tests for site-specific positive selection in metabolic candidate genes imply that the observed physiological differences are adaptive and thus likely correspond to ecological niches available to each symbiont group. These findings highlight the role of niche differentiation in creating divergent paths of reductive genome evolution in vertically transmitted symbionts.

genomics↗

bioRxiv2020

Deep-sea mussels from a hybrid zone on the Mid-Atlantic Ridge host genetically indistinguishable symbionts

The composition and diversity of animal microbiomes is shaped by a variety of factors, many of them interacting, such as host traits, the environment, and biogeography. Hybrid zones, in which the ranges of two host species meet and hybrids are found, provide natural experiments for determining the drivers of microbiome communities, but have not been well studied in marine environments. Here, we analysed the composition of the symbiont community in two deep-sea, Bathymodiolus mussel species along their known distribution range at hydrothermal vents on the Mid-Atlantic Ridge, with a focus on the hybrid zone where they interbreed. In-depth metagenomic analyses of the sulphur-oxidising symbionts of 30 mussels from the hybrid zone, at a resolution of single nucleotide polymorphism analyses of [~]2500 orthologous genes, revealed that parental and hybrid mussels have genetically indistinguishable symbionts. While host genetics does not appear to affect symbiont composition in these mussels, geographic location of the mussels on the Mid-Atlantic Ridge explained 45 % of symbiont genetic variability based on redundancy analyses. We hypothesize that geographic structuring of the free-living symbiont population plays a major role in driving the composition of the microbiome in these deep-sea mussels.

microbiology↗

bioRxiv2019

Host-microbe interactions in the chemosynthetic Riftia pachyptila symbiosis

The deep-sea tubeworm Riftia pachyptila lacks a digestive system, but completely relies on bacterial endosymbionts for nutrition. Although the symbiont has been studied in detail on the molecular level, such analyses were unavailable for the animal host, because sequence information was lacking. To identify host-symbiont interaction mechanisms, we therefore sequenced the Riftia transcriptome, which enabled comparative metaproteomic analyses of symbiont-containing versus symbiont-free tissues, both under energy-rich and energy-limited conditions. We demonstrate that metabolic interactions include nutrient allocation from symbiont to host by symbiont digestion, and substrate transfer to the symbiont by abundant host proteins. Our analysis further suggests that Riftia maintains its symbiont by protecting the bacteria from oxidative damage, while also exerting symbiont population control. Eukaryote-like symbiont proteins might facilitate intracellular symbiont persistence. Energy limitation apparently leads to reduced symbiont biomass and increased symbiont digestion. Our study provides unprecedented insights into host-microbe interactions that shape this highly efficient symbiosis.

systems biology↗