FEMS Microbiology Ecology

Soil organic matter is the largest terrestrial reservoir of organic carbon. Its particulate fraction, particulate organic matter (POM), serves as a resource and surface for microbial colonization. Degradation of complex biopolymers like cellulose and chitin requires extracellular enzymes produced by phylogenetically diverse microbes. Despite their importance for carbon cycling, the structure and spatio-temporal dynamics of POM-associated microbial communities in soil and how specific substrates influence them remain poorly understood. This study investigated whether microbial communities associated with POM change in composition and richness over time and whether chitin and cellulose select for distinct fungal and bacterial taxa. We incubated self-manufactured, millimetre-sized model substrate particles containing chitin or cellulose in soil under laboratory and field conditions. We assessed particle-associated communities at multiple time points over a 50-day-long incubation in the lab and after 47 days in the field. Our results show that community structure and temporal dynamics of particle-associated microbial communities were substrate-specific. While microbial biomass increased on both particle types, chitin-associated microbial communities exhibited stronger temporal changes. Communities on chitin and cellulose particles were enriched in specific bacterial and fungal genera compared to communities in the surrounding soil. We demonstrate that microbial communities associated with model chitin particles underwent notable temporal changes, including decreased microbial richness and shifts in community composition over the incubation period. This study shows the potential of model particles to advance our understanding of particle- and substrate-associated microbial communities in soil.

Environmental change, especially frequent droughts, is predicted to detrimentally impact the North American perennial grasslands. Consistent dry spells will affect plant communities as well as their associated rhizobiomes, possibly altering the plant host performance under environmental stress. Therefore, there is a need to understand the impact of drought on the rhizobiome, and how the rhizobiome may modulate host performance and ameliorate its response to drought stress. In this study, we analyzed bacterial and fungal communities in the rhizospheres of three ecotypes (dry, mesic, and wet) of a dominant prairie grass, Andropogon gerardii. The ecotypes were established in 2010 in a common garden design and grown for a decade under persistent dry conditions at the arid margin of the species range in Colby Kansas. The experiment aimed to answer whether and to what extent do the different ecotypes maintain or recruit distinct rhizobiomes after ten years in an arid climate. In order to answer this question, we screened the bacterial and fungal rhizobiome profiles of the ecotypes under the arid conditions of western KS as a surrogate for future climate environmental stress using 16S rRNA and ITS2 metabarcoding sequencing. Under these conditions, bacterial communities differed compositionally among the A. gerardii ecotypes, whereas the fungal communities did not. The ecotypes were instrumental in driving the differences among bacterial rhizobiomes, as the ecotypes maintained distinct bacterial rhizobiomes even after ten years at the edge of the host species range. This study will aid us to optimize plant productivity through the use of different ecotypes under future abiotic environmental stress, especially drought.

Polyploidy--whole genome duplication--is common in plants. Studies over the last several decades have documented numerous mixed-ploidy populations. Whether arising via recurrent whole genome duplication events within a population, or from secondary contact, the persistence of mixed populations depends on the ability of the minority cytotype to overcome the negative frequency dependent effects of outcrossing with other ploidies, known as Minority Cytotype Exclusion. One mechanism of overcoming Minority Cytotype Exclusion is microbially-mediated niche differentiation (MMND), wherein cytotypes occupy different niches via interactions with different sets of microbes. Inherently cryptic, MMND is underexplored in polyploid plant populations. Here, we search for evidence of MMND in creosotebush (Larrea tridentata), a dominant desert shrub of the southwestern U.S. and northern Mexico. We sequenced fungi from rhizosphere soils of diploid, autotetraploid, and autohexaploid plants growing in two naturally-occurring mixed-cytotype populations. Within populations, we found substantial fungal assemblage overlap across host plant cytotypes. However, using indicator species analysis, we identified some fungi that are differentiated by host plant cytotype, satisfying a precondition for MMND. Future study is needed to determine the degree of niche differentiation conferred, if any, and whether the identified fungi play a role in the long-term persistence of multiple cytotypes within populations.

The spermosphere is the transient, immediate zone of soil around imbibing and germinating seeds. It represents a habitat where there is contact between seed-associated microbes and soil microbes, but is studied less compared to other plant habitats. Previous studies on spermosphere microbiology were primarily culture-based or did not sample the spermosphere soil as initially defined in space and time. Thus, the objectives of this study were to develop an efficient strategy to collect spermosphere soils around imbibing soybean and cotton in non-sterile soil and investigate changes in microbial communities. The method employed sufficiently collected spermosphere soil as initially defined in space by constraining the soil sampled with a cork borer and confining the soil to a 12-well microtiter plate. Spermosphere prokaryote composition changed over time and depended on the crop within six hours after seeds were sown. By 12 to 18 hours, crops had unique microbial communities in spermosphere soils. Prokaryote evenness dropped following seed imbibition with the proliferation of copiotrophic soil bacteria. Due to their long history of plant growth promotion, prokaryote OTUs in Bacillus, Paenibacillus, Burkholderia, Massilia, Azospirillum, and Pseudomonas were notable genera enriched. Fungi and prokaryotes were hub taxa in cotton and soybean spermosphere networks. Additionally, the enriched taxa were not hubs in networks, suggesting other taxa besides those enriched may be important for spermosphere communities. Overall, this study advances knowledge in the assembly of the plant microbiome early in a plants life, which may have plant health implications in more mature plant growth stages.

The built environment houses diverse microbial communities whose diversity and composition differ among building materials and environmental conditions. Ecological theory makes predictions about how productivity and diversity shape communities, and experiments in the built environment provide an opportunity to test these. We manipulated moisture (constant or repeated wet-dry cycling) on three common building materials to test predictions about alpha and beta diversity. The most productive material (oriented strand board) supported the highest bacterial alpha and beta diversity, and these diversity levels were reduced by repeated drying disturbances. Diversity patterns for fungi were more variable, with the highest alpha diversity on low-moderate productivity material (gypsum wallboard). Fungal beta diversity was reduced by disturbance on high-productivity material, but increased on the other materials. These patterns were driven largely by members of Bacillaceae, Sphingomonadaceae, and Aspergillaceae that reached high abundances in some treatments. Differences between bacteria and fungi may be due to the scale-dependence of productivity-diversity relationships. Together, these results indicate that disturbances can interact with building materials, in some cases leading to variation in community composition that makes it difficult to predict the conditions under which microorganisms with potential importance to health and safety will occur. ImportanceThe built environment--the homes, workplaces, vehicles, and other spaces where people spend most of their time--contains an enormous diversity of microorganisms with significance for human wellbeing, yet we know little about the factors shaping these microbial communities. We found that patterns of wetting and drying that mimic indoor leaks on common building materials affects the diversity of bacteria and fungi growing on the materials. But the identity of these microorganisms differed from one building material to another, and this was especially variable with wetting and drying. This means that common disturbances that lead to microbial growth in homes and offices can make it difficult to predict which microbes, including those that represent health threats to people, will occur in the built environment.

Microorganisms play crucial roles in the lives of metazoans and can significantly impact host fitness. However, recent evidence suggests that many species may lack microorganisms that are positively associated with host fitness. Assessing the prevalence of host-specific microbiomes in animals has proven challenging due to limited studies in most higher taxa, with most investigations focusing on microbes in mammals, cephalopods, fish, and corals. This knowledge gap extends to springtails (Arthropoda: Collembola), which are widespread and abundant hexapods found in terrestrial and semi-aquatic habitats, contributing to important ecological functions. Here we investigated taxonomic bycatch in genome sequences generated from entire individuals of 70 springtail species. We aimed to understand whether microbial and other taxa associated with springtails are influenced by host phylogeny and environmental parameters. The analyses revealed high richness of bacteria and other taxa in the analyzed sequences, but detected no phylosymbiotic or environmental filtering signal in community composition. The findings suggest that springtails may be one of potentially many animal groups lacking distinct microbiomes. The study demonstrates how entire eukaryotic groups can be tested for phylosymbiotic patterns with taxonomic bycatch from genome sequences.

Mycorrhizal fungi form ubiquitous symbiotic associations with almost all land plants and are of key interest to evolutionary biologists and ecologists because this ancient symbiosis was essential for the colonization of land by plants - a major turning point in the evolutionary history of the earth - and the subsequent development and functioning of the terrestrial ecosystems. Within the orchid family (Orchidaceae), plants establish unique interactions with specific orchid mycorrhizal fungi. These fungal symbionts are essential for the development of orchids as they provide carbon and soil nutrients to germinating orchid seeds and the nutritional supply continues for adult orchids to different degrees. Fueled by the development of DNA sequencing techniques, the diversity of mycorrhizal and other root-associated fungi in orchid roots has been extensively reported in evolutionary and ecophysiological studies. However, the full taxonomic range of orchid-associated fungi remains to be investigated in a broad phylogenetic framework, hampering a further understanding of the evolution and ecological adaptation of orchid mycorrhizal interactions. In this study, we used the most complete DNA dataset to date to map the phylogenetic distribution and ecological lifestyles of root-associated fungi in Orchidaceae by phylogenetic reconstructions at the fungal order level. We found that a broad taxonomic range of fungi (clustered into 1898 operational taxonomic units) resided in orchid roots, belonging to at least 150 families in 28 orders in Basidiomycota and Ascomycota. These fungi were assigned to diverse ecological lifestyles including typical orchid mycorrhizal fungi ( rhizoctonia), ectomycorrhizal fungi, wood- or litter-decaying saprotrophic fungi, and other endophytes/pathogens/saprotrophs. This overview reveals that among the four different mycorrhizal types, the orchid mycorrhizal symbiosis probably involves the highest diversity of fungal taxa. We hope that our newly reconstructed phylogenetic framework of orchid-associated fungi and the assessment of their potential mycorrhizal status will benefit future ecological and evolutionary studies on orchid-fungal interactions.

Fungi play important roles in biofilms, are very versatile in their ecological role, and are considered as plastic degraders. Here we aim to increase the resolution of the fungal members of the Plastisphere, to understand fungal substrate specificities and related potential ecological impacts. Fifteen-month-old fungal Plastisphere communities were investigated on 9 different plastic types and glass in seawater from the North Sea. By integrating scanning electron microscopy (SEM) imaging, ITS-based fingerprinting, and re-evaluated 18S rRNA gene sequence data through a fungal-specific phylogeny-based pipeline, we observed fungal Plastispheres and identified specific characteristics based on morphotypes, phylogeny, and biodiversity across different substrate types. Plastic types selected for specific fungal communities with polyolefine communities indicating significantly higher diversity compared to all other plastic types. Furthermore, specific plastic types may select for specific fungal taxa and their potential hosts, highlighting the complexity of marine biofilm food webs, and related ecological implications.

In this study, we explore the relationship between ecologically distinct soil microbiomes and their role in plant growth promotion through organic matter (OM) decomposition. Using a controlled experimental system, we tested whether living microbiomes from geographically and ecologically distinct environments impact plant biomass when provided with OM in the form of dried, ground leaves. Results showed a consistent threefold increase in plant biomass when a living microbiome and organic matter were present, regardless of the microbiomes origin, which included agricultural fields, desert soil, and pine-oak forest soil, municipal compost, and the microbiome on unautoclaved organic matter. Bacterial community profiling based on 16S amplicon sequencing revealed genera, e.g. Massilia, that were significantly associated with decomposition and subsequent plant growth promotion. This suggests a conserved functional capacity for organic matter decomposition across diverse microbiomes, likely due to evolutionary pressures to efficiently break down plant material for nutrient acquisition. The study provides a framework for further investigation into microbial consortia that enhance plant growth via decomposition, offering a robust experimental system to identify microbes and microbial processes that could be harnessed to improve nutrient uptake from organic inputs like cover crops.

The assembly and successional processes of microbial communities inhabiting deep-sea whale and wood falls are highly complex and vastly unknown, as a myriad of factors may affect the development of a chemosynthetic-based ecosystem on these organic islands. The chemoautotrophy supported by organic substrates is the basis of long-lasting ecosystems, considered biodiversity hotspots in the oligotrophic deep sea. Understanding how these microbial communities develop and the factors affecting them could shed light on processes related to the maintenance of biodiversity in this environment. We performed a whale- and wood-fall experiment in the southwest Atlantic on the Brazilian continental margin and investigated biofilm-forming bacterial and archaeal communities colonising these substrates, deployed at 1500 and 3300 m depth. The composition of the prokaryotic communities shared some similarities with previously reported organic falls in the north Pacific and the Mediterranean Sea, mainly regarding sulphur oxidising chemolithotrophic taxa from the phyla Campylobacterota and Proteobacteria. Communities were found to be highly different between the organic substrates, as whale fall associated biofilms presented a higher dominance of sulphur oxidising chemolithotrophs. We also observed a significant difference between the two sites, with the whale associated communities at the 1500 isobath presenting a faster establishment of the chemosynthetic taxa.

Seagrasses are the only plants that flower and produce seeds in the marine environment, where they form vast meadows that fulfill important ecosystem functions. Yet, seagrass cover has declined in many coastal areas around the world and re-colonization is slow. Despite clonal growth, seed recruitment is essential for seagrass dispersal and regional genetic diversity. While the seed microbiome of several terrestrial plants has been shown to influence germination and seedling survival, the role of the seagrass seed microbiome is still unclear. We investigated the microbiome of eelgrass (Zostera marina) seeds, leaves and roots along the natural salinity gradient of the German North and Baltic Sea coasts. Despite this strong variability, Z. marina seeds harbor distinct prokaryotic and eukaryotic microbial communities compared to those on leaves and roots. Predicted microbial functions suggest roles in nutrient cycling and germination, which may be critical for recovery and restoration of seagrass ecosystems. Scientific significance statementSeagrass meadows are important but declining coastal ecosystems. Around the world, efforts are being made to restore seagrass meadows in order to halt the loss of biodiversity and maintain ecosystem function. With an evolutionary history on land, seagrasses have introduced unique features to the marine environment, such as seeds. In terrestrial plants, the seed microbiome has been shown to be important for seed germination and seedling health. Here we show that the northern hemisphere seagrass Zostera marina has a distinct seed microbiome, containing core bacterial and eukaryotic taxa and predicted functions that may play a role in seed germination and vertical microbiome transmission. Our results lay the foundation for future seagrass restoration efforts that seek to manipulate seed microbiomes to improve seedling survival. Data availability statementRaw DNA sequence data has been deposited in the European Nucleotide Archive (ENA) at EMBL-EBI under accession number PRJEB72211. Processed data and associated metadata will be made available on PANGEA via the German Federation for Biological data (GFBio.org).

High tunnels and open-field systems differ markedly in soil physicochemical properties, yet their effects on belowground microbiomes remain poorly understood. We characterized bacterial and fungal communities in paired high-tunnel and adjacent field soils from 100 small-scale vegetable farms across Minnesota, integrating amplicon sequencing of 16S rRNA and ITS2 regions with soil nutrient data, arbuscular mycorrhizal fungi (AMF) spore counts, and microbial co-occurrence networks. High-tunnel soils had higher pH, organic matter, and multiple macronutrients (notably P, K, and N forms) and lower bulk density than fields, reflecting intensive organic amendments and reduced leaching. Despite these differences, bacterial and fungal alpha diversity did not differ between environments, whereas beta diversity analyses revealed strong shifts in community composition. High tunnels were enriched in salt- and stress-tolerant bacterial phyla (Firmicutes, Deinococcota, Patescibacteria, Halanaerobiaeota, Halobacterota) and saprotrophic fungal groups (Mortierellomycota, Ascomycota, Basidiomycota, Mucoromycota), while several oligotrophic or symbiotic taxa, including Acidobacteriota and Glomeromycota, declined. Glomeromycota relative abundance was negatively correlated with high soil phosphorus, whereas AMF spore densities did not decline, suggesting suppression of active mycorrhizal symbioses rather than propagule loss under high-nutrient conditions. Co-occurrence network analyses showed that bacterial and fungal networks in high tunnels were less dense, more modular, and exhibited higher ratios of positive to negative associations than field networks, consistent with stress-induced shifts toward more facilitative interactions. Collectively, our results indicate that high-tunnel production homogenizes soil microbiomes and selects for stress- and high-nutrient-adapted taxa, with potential consequences for nutrient cycling, AMF function, and long-term agroecosystem outcomes.

Saccharomyces paradoxus is a model organism in ecology and evolution. However, its metabolism in its native habitat remains mysterious: it is frequently found growing on leaf litter, a habitat with few carbon sources that S. paradoxus can metabolize. We hypothesized that leaf-decomposing fungi from the same habitat break down the cellulose in leaf litter extracellularly and release glucose, supporting S. paradoxus growth. We found that facilitation by leaf-decomposing fungi was possible on cellulose and inhibition was common on glucose, suggesting diverse interactions between S. paradoxus and other fungi that have the potential to support S. paradoxus in nature.

A live microbial culture is invaluable to assess traits and functions, yet culturing immediately from fresh soil is logistically challenging and media selection is not trivial. Deeper ecological understanding of pyrophilous microbes and their traits is hampered by a lack of culture-based work causing researchers to rely heavily on community sequence analysis. To improve our understanding of isolating pyrophilous bacteria and fungi after wildfires from burned soil, we tested which: 1) soil storage method and 2) media retained highest genera richness and highest culturable viability as measured by CFUs retained. We tested four soil storage methods (dried, refrigerated at 4{degrees}C, stored at -80{degrees}C with or without glycerol) using a well-homogenized soil sample, plated microbes on rich media, and compared to fresh soil obtained 6 months after a severe California shrubland wildfire. From the fresh soils, we tested 3 media types: rich (Lysogeny Broth (LB) for bacteria; Malt Yeast Agar (MYA) for fungi), oligotrophic (Reasoners 2 Agar (R2A)) and media made from pyrogenic organic matter (PyOM). For bacteria, storing soil frozen at -80{degrees}C without glycerol yielded the highest genera richness and with glycerol preserved the most species. For fungi, storing soil at -80{degrees}C without glycerol preserved the most species but preserved equivalent richness of genera as fresh and 4{degrees}C soil. R2A yielded the highest bacterial and fungal genus richness but some species of interest were only captured with PyOM. Using a combination of these storage and media methods along with a few additional techniques (mushroom cultivation, smoke cultivation, etc.) from 2018-2022, we cultured >500 isolates (286 bacteria; 258 fungi) after 7 California wildfires for testing pyrophilous microbial traits. ImportanceFires are increasing in frequency and severity across the globe, making the understanding of the traits of the pyrophilous microbes that survive and thrive post-fire and influence post-fire ecosystem regeneration critical and pressing. Yet, our ability to characterize the traits of pyrophilous microbes through genomics, transcriptomics, and phenotypic assays is hampered by lack of organisms in culture. Here, we debut a new medium created from pyrogenic organic matter that helps to cultivate fastidious pyrophilous microbes, and also describe a large-scale culture collection of pyrophilous bacteria and fungi (>500 isolates) that can be used for future collaborative research. We comprehensively test how soil storage and media type affect the cultivation of both bacteria and fungi, and for the first time, we test the best method to store soil to retain fungal diversity. Our work can be applied to improve culture collections of fastidious microbes from a variety of environments.

The contribution of predation between bacteria to microbial community dynamics in agricultural fields has hardly been investigated. Here. dynamics of general prokaryotes (GEP) and of the predators Bdellovibrionales (Bd) and Bacteriovoracales (Bac) (Bdellovibrio-and-Like Organisms, BALOs) were studied in two agricultural fields differing in organic and mineral input regimes, for one year. Season, but not fertilization, affected absolute sizes of GEP and of BALO communities. 16S rRNA gene community analysis identified numerous novel Bd and Bac lineages, with none of the dominant BALOs related to characterized isolates. A few dominant BALO amplicon sequence variants (ASVs) persisted year-round, whereas others showed seasonal- or treatment specific responses. GEP, Bd, and Bac ASV a-diversity was mostly influenced by season, with some changes due to fertilization in Bd, and Bac communities. Seasonal changes, site, and fertilization regimes influenced {beta}-diversity of GEP, Bd and Bac communities and determined the structure of BALO-gram-negative bacteria interaction networks, signaling that niche segregation acts at the microbiome-BALO interface. Accordingly, we suggest that shifts in GEP community structure triggered by environmental changes and agricultural practices cascade to BALO predators, in turn affecting BALO-microbiome interactions. These dynamics may be harnessed to manipulate the soil microbiome to benefit sustainable environmental and agricultural outcomes.

How symbiotic bacteria coordinate and respond to their hosts during complex life cycle transitions is a fascinating and unresolved topic, particularly for organisms that exist solely in natural environments, where their intricate life cycles make laboratory cultivation extremely challenging. Complex life cycles are often associated with host alternation in aphids, especially in eriosomatine gall-forming aphids, which exhibit seven distinct morphs throughout their life cycle while shifting their host plants seasonally. Despite these dramatic changes, these aphids maintain the obligate symbiotic bacterium, Buchnera aphidicola, to enhance their nutritional status. The bacterial communities in our wild-derived samples were dominated by aphid symbionts, including Buchnera, Regiella inseticola, Wolbachia, Arsenophonus, and Serratia symbiotica. Buchnera and Regiella prevailed in Tetraneura akinire and Tetraneura sorini, while Buchnera and Arsenophonus were more abundant in Eriosoma harunire. Our study, utilizing 16S rRNA metagenomic sequencing on the aphid Tetraneura akinire, demonstrates that Buchnera plays significant roles during most life cycle stages but is absent during the sexual male stage, where it is replaced by Regiella. Moreover, Buchnera densities exhibit significant variability across the aphids life cycles and are notably lower in gall generations. This result contradicts the previous hypothesis that galls provide superior nutrition compared to aphids in grassroot-feeding generations. In this study, we reveal the dynamics of symbiotic bacteria across the complex life cycles of three eriosomatine aphid species that form galls on the same Japanese elm tree, Ulmus davidiana var. japonica. Within the framework of tripartite symbiosis, the seemingly passive symbiotic bacteria adjust the hosts specific life stages and influence the changing host ecology in a cascading manner.

O_LIGlacier forefields in the high-desert region of Ladakh (northwestern Himalaya) are colonized by a variety of interdependent organisms, including lichens, prokaryotes, fungi, mosses, and vascular plants, along a successional gradient. Together with bulk soil, these hosts and their associated microorganisms form a broader microbial metacommunity (holobiome) whose structure, interactions and functions remain poorly underexplored in one of the Earths most extreme and climate-sensitive environments. C_LIO_LIUsing a multidisciplinary approach combining glacial chronosequence transects, GIS-derived topographic variables, soil properties, and plot cover measurements, we assessed the abiotic and biotic factors influencing bacterial and fungal communities sequenced from different hosts and bulk soil (hereafter sources). Microbial composition was primarily shaped by source identity, though certain sources, such as biological soil crusts (BSCs), mosses, and plant rhizospheres, also showed relationships with moraine age in either bacterial or fungal communities. C_LIO_LIBacterial and fungal community congruence was tested using Procrustes analyses, revealing that mosses maintained tightly coupled inter-kingdom relationships throughout the glacier forefields. However, the degree of congruence in plant rhizospheres and bulk soils was influenced by topographic variation and moraine age, respectively. C_LIO_LICo-occurrence network analyses revealed that early successional microbial communities were assembled more stochastically, with bacteria being more interconnected than fungi. In contrast, late successional stages were more compartmentalized, being more structurally stabile, likely driven by increased plant cover and functional redundancy among microbial taxa. C_LIO_LIKeystone bacterial and fungal taxa were identified in plant rhizospheres and bulk soil using a dual-criteria approach related to inter-kingdom congruence and network node eigenvalues. Furthermore, some of these taxa were associated with environmental factors, suggesting topographic heterogeneity and successional age can promote or deter the influence of keystone taxa. C_LIO_LISynthesis: This study reveals the impact of both macroorganism colonization (i.e. plants, mosses, and lichens) and microcommunity establishment (BSCs and bulk soil), as abiotic and biotic sources, on microbial metacommunity assembly in glacier forefields. By adopting a broader approach across different spatial scales, we demonstrate that while plant colonization plays a central role in shaping microbial metacommunities, its effects are modulated by topographic variation along the chronosequence. C_LI

Permafrost soils store a substantial part of the global soil carbon and nitrogen. However global warming causes abrupt erosion and gradual thaw, which make these stocks vulnerable to microbial decomposition into greenhouse gases. Here, we investigated the microbial response to abrupt in situ permafrost thaw. We sequenced the total RNA of a 1 m deep soil core consisting of up to 26500-year-old permafrost material from an active abrupt erosion site. We analysed the microbial community in the active layer soil, the recently thawed, and the intact permafrost and found maximum RNA:DNA ratios indicating a microbial bloom in recently thawed permafrost. Several fast-growing prokaryotic taxa dominated thawed permafrost, including Sphingobacteriales, Burkholderiales, and Nitrosomonadales. Overall, the thaw state and soil moisture consistently explained changes in community composition, with especially the permafrost community being significantly distinct from thawed soils. Predation correlated with changes in prokaryotic composition. Bacterial grazers were dominated by Myxococcales and abundant in the active layer. In contrast, protozoa, especially Cercozoa and Ciliophora, doubled in relative abundance in thawed layers. Our findings highlight the ecological importance of a rapid development of microbial blooms as well as the successive predation as biological control mechanism in abruptly thawing permafrost. One sentence summaryUsing total RNA from an up to 26500-year-old abruptly eroding permafrost site in Greenland, we described a microbial bloom and its controls, including bacterial and microeukaryotic predators. O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=146 SRC="FIGDIR/small/499897v2_ufig1.gif" ALT="Figure 1"> View larger version (51K): org.highwire.dtl.DTLVardef@10ab79eorg.highwire.dtl.DTLVardef@9d0146org.highwire.dtl.DTLVardef@1bec509org.highwire.dtl.DTLVardef@179f397_HPS_FORMAT_FIGEXP M_FIG C_FIG

Most multicellular organisms harbor microbial colonizers that provide various benefits to their hosts. Although these microbial communities may be host species- or even genotype-specific, the associated bacterial communities can respond plastically to environmental changes. In this study, we estimated the relative contribution of environment and host genotype to bacterial community composition in Nematostella vectensis, an estuarine cnidarian. We isolated N. vectensis polyps from five different populations along a north-south gradient on the Atlantic coast of the United States and Canada at three different times of the year. While half of the polyps were immediately analyzed for their bacterial composition by 16S rRNA gene sequencing, the remaining polyps were cultured under laboratory conditions for one month. Bacterial community comparison analyses revealed that laboratory maintenance reduced bacterial diversity by fourfold, but maintained a population-specific bacterial colonization. Interestingly, the differences between bacterial communities correlated strongly with seasonal variations, especially with ambient water temperature. To decipher the contribution of both ambient temperature and host genotype to bacterial colonization, we generated 12 clonal lines from six different populations in order to maintain each genotype at three different temperatures for three months. The bacterial community composition of the same N. vectensis clone differed greatly between the three different temperatures, highlighting the contribution of ambient temperature to bacterial community composition. To a lesser extent, bacterial community composition varied between different genotypes under identical conditions, indicating the influence of host genotype. In addition, we identified a significant genotype x environment interaction determining microbiota plasticity in N. vectensis. From our results we can conclude that N. vectensis-associated bacterial communities respond plastically to changes in ambient temperature, with the association of different bacterial taxa depending in part on the host genotype. Future research will reveal how this genotype-specific microbiota plasticity affects the ability to cope with changing environmental conditions.

The Dark Zone of the western Greenland Ice Sheet is the most expansive region of contiguous bare terrestrial ice in the Northern Hemisphere. Microbial processes within the Dark Zone play an important role in driving extensive albedo reduction and amplified melting, yet the composition and function of those consortia have not been fully identified. Here we present the first results from joint 16S rRNA gene and 16S rRNA (cDNA) analysis for the comparison of input (snow), storage (cryoconite), and output (supraglacial stream water) habitats across the Dark Zone over the melt season. Our analysis reveals that all three Dark Zone communities are characterized by a preponderance of rare taxa exhibiting high protein synthesis potential (PSP). Furthermore, taxa with high PSP represent highly connected \"bottlenecks\" within community structure, consistent with roles as metabolic hubs within their communities. Finally, the detection of low abundance-high PSP taxa affiliated with Methylobacterium within snow and stream water indicates a potential role for Methylobacterium in the carbon cycle of Greenlandic snowpacks, and importantly, the export of potentially active methylotrophs to the bed of the Greenland Ice Sheet. By comparing the dynamics of bulk and potentially active microbial communities in the Dark Zone of the Greenland Ice Sheet our study provides insight into the mechanisms and impacts of the microbial colonization of this critical region of our melting planet.