Diverse Microbial Assemblages Research Articles

Sensitivity of the mangrove-estuarine microbial community to aquaculture effluent

SummaryMangrove-dominated estuaries host a diverse microbial assemblage that facilitates nutrient and carbon conversions and could play a vital role in maintaining ecosystem health. In this study, we used 16S rRNA gene analysis, metabolic inference, nutrient concentrations, and δ13C and δ15N isotopes to evaluate the impact of land use change on near-shore biogeochemical cycles and microbial community structures within mangrove-dominated estuaries. Samples in close proximity to active shrimp aquaculture were high in NH4+, NO3− NO2−, and PO43−; lower in microbial community and metabolic diversity; and dominated by putative nitrifiers, denitrifies, and sulfur-oxidizing bacteria. Near intact mangrove forests we observed the presence of potential nitrogen fixers of the genus Calothrix and order Rhizobiales. We identified possible indicators of aquaculture effluents such as Pseudomonas balearica, Ponitmonas salivibrio, family Chromatiaceae, and genus Arcobacter. These results highlight the sensitivity of the estuarine-mangrove microbial community, and their ecosystem functions, to land use changes.

Soil bacterial diversity based on management and topography in a silvopastoral system

Soil microorganisms play crucial roles in nutrient cycling and provisioning ecosystem services. However, little is known about how soil microbial communities are affected by soil management and landscape position in silvopastures. The current study aimed to understand effects of forage species [non-native, cool season orchardgrass (Dactylis glomerata L.) and a warm-season native grass mix (Andropogon gerardii L. and Schizachyrium scoparium L.) planted in strips between hedgerows], soil fertility (poultry litter and a control), and soil moisture regimes (aquic and udic) on soil bacterial communities to evaluate linkages between terrain attributes and soil bacterial assemblages. Thirteen terrain attributes representing topographic variability were clustered into four topographic functional units (TFUs) using the k-means method, and their impact on soil microbial diversity was evaluated. Illumina sequencing results identified a soil moisture regime × forage species interaction, with native grass species under wet (aquic) conditions resulting in the most diverse microbial assemblages relative to dry (udic) and wet soil conditions for the non-native forage (orchardgrass). These results suggest an enhanced soil microbial diversity under native grasses with greater available soil water. Overall, microbial diversity was negatively correlated with elevation, suggesting niche differentiation and microbial preference for lower elevations. Overall, TFUs and selected terrain attributes may be useful for predicting microbiota dynamics in integrated tree-livestock systems.

Taxonomic and functional analyses reveal existence of virulence and antibiotic resistance genes in beach sand bacterial populations.

Coastal sands are important natural recreational facilities that have become hotspots for tourism and economic development. However, these sands harbour diverse microbial assemblages that play a critical role in the balance between public health and ecology. In this study, targeted high-throughput sequencing analysis was used to identify sand-borne bacterial populations at four public beaches in Durban. The effect of heavy metal in shaping the distribution of bacterial metacommunities was determined using canonical correspondence analysis (CCA), while the functional gene profiles were predicted using PICRUSt2 analysis. Sequences matching those of the bacterial phylum Proteobacteria were the most abundant in all samples, followed by those of the phyla Firmicutes, Actinobacteria, Bacteroidetes, and Gemmatimonadetes. Genus-level taxonomic analysis showed the presence of 1163 bacterial genera in all samples combined. The distribution of bacterial communities was shaped by heavy metal concentrations, with the distribution of Flavobacteria, Bacteroidia, and Deltaproteobacteria influenced by Pb and Zn, while B and Cr influenced the distribution of Clostridia and Gammaproteobacteria, respectively. Identified antibiotic resistance genes included the peptidoglycan biosynthesis gene II, III, IV, and V, as well as the polymyxin resistance gene, while the virulence genes included the sitA, fimB, aerobactin synthase, and pilL gene. Our findings demonstrate that beach sand-borne bacteria are reservoirs of virulence and antibiotic resistance genes. Contamination of beach sands with heavy metals selects for both heavy metal resistance and antibiotic resistance in beach sand bacterial communities. Children and immunocompromised people engaging in recreational activities on beaches may be exposed to higher risk of infection.

Microbiome dynamics in the tissue and mucus of acroporid corals differ in relation to host and environmental parameters.

Corals are associated with diverse microbial assemblages; however, the spatial-temporal dynamics of intra-species microbial interactions are poorly understood. The coral-associated microbial community varies substantially between tissue and mucus microhabitats; however, the factors controlling the occurrence, abundance, and distribution of microbial taxa over time have rarely been explored for different coral compartments simultaneously. Here, we test (1) differentiation in microbiome diversity and composition between coral compartments (surface mucus and tissue) of two Acropora hosts (A. tenuis and A. millepora) common along inshore reefs of the Great Barrier Reef, as well as (2) the potential linkage between shifts in individual coral microbiome families and underlying host and environmental parameters. Amplicon based 16S ribosomal RNA gene sequencing of 136 samples collected over 14 months, revealed significant differences in bacterial richness, diversity and community structure among mucus, tissue and the surrounding seawater. Seawater samples were dominated by members of the Synechococcaceae and Pelagibacteraceae bacterial families. The mucus microbiome of Acropora spp. was dominated by members of Flavobacteriaceae, Synechococcaceae and Rhodobacteraceae and the tissue was dominated by Endozoicimonaceae. Mucus microbiome in both Acropora species was primarily correlated with seawater parameters including levels of chlorophyll a, ammonium, particulate organic carbon and the sum of nitrate and nitrite. In contrast, the correlation of the tissue microbiome to the measured environmental (i.e., seawater parameters) and host health physiological factors differed between host species, suggesting host-specific modulation of the tissue-associated microbiome to intrinsic and extrinsic factors. Furthermore, the correlation between individual coral microbiome members and environmental factors provides novel insights into coral microbiome-by-environment dynamics and hence has potential implications for current reef restoration and management efforts (e.g. microbial monitoring and observatory programs).

Screening and activity of yeast-associated with cocoa-bean fermentation against phytopathogenic yeast and fungi

Cocoa-bean fermentation has been associated with the involvement of diverse microbial assemblages which consist of a wide array of bacteria and yeast. We attempted to screen and to identify the potential antifungal yeast from this assemblage against phytopathogenic fungi. We employed in-vitro antagonism assay using agar plug methods to performpreliminary screening from 35 yeast isolates followed by total protein production and measurement with Bradford methods. We found three yeast strains that were effective against Trichoderma sp. T009, and two moulds associated with cocoa (Penicilliumsp. Cocoa2 and Fusariumsp.Cocoa 1). The three bioactive yeast strains were identified as Saccharomyces cerevisiae IDI-002, Hanseniasporauvarum IDE-056 and Hanseniasporauvarum IDE-271 based on molecular identification and phylogenetic analysis. The production of antifungal protein from pure cultures on YEPG media resulted intotal protein concentration between 6.20 - 8.17 mg/L. Cell suspension showed higherinhibitory activity compared to thecell-free supernatant gave indication that antifungal proteins in the bulk fermentation was below the minimal inhibitory concentration to cause the inhibitory effect. Further characterization, purification, and optimization are still needed before the up-scale production of antifungal metabolites and its biological control application.

Environmental Filtering Drives the Assembly of Habitat Generalists and Specialists in the Coastal Sand Microbial Communities of Southern China.

Coastal sands harbor diverse microbial assemblages that play a critical role in the biogeochemical cycling of beach ecosystems. However, little is known about the relative importance of the different ecological processes underlying the assembly of communities of sand microbiota. Here, we employed 16S rDNA amplicon sequencing to investigate the sand microbiota of two coastal beaches, in southern China. The results showed that sand microbial assemblages at intertidal and supratidal zones exhibited contrasting compositions that can be attributed to environmental filtering by electric conductivity. A consistent pattern of habitat generalists and specialists of sand microbiota was observed among different beach zones. Null and neutral model analyses indicated that the environmental filtering was mainly responsible for supratidal microbial communities, while the neutral processes could partially influence the assembly of intertidal communities. Moreover, environmental filtering was found to shape the habitat specialists, while random dispersal played a major role in shaping generalists. The neutral model analysis revealed that the habitat generalists exceeding the neutral prediction harbored a relatively higher proportion of microbial taxa than the specialist counterparts. An opposite pattern was observed for taxa falling below the neutral prediction. Collectively, these findings offer a novel insight into the assembly mechanisms of coastal sand microbiota.

Microbial Diversity Exploration of Marine Hosts at Serrana Bank, a Coral Atoll of the Seaflower Biosphere Reserve

Microorganisms represent nearly 90% of ocean biomass and are fundamental for the functioning and health of marine ecosystems due to their integral contribution to biogeochemical cycles and biological processes. In marine environments, microorganisms exist as microbial communities in the water column, benthonic substrates and macroorganisms, where they establish symbiotic interactions and fulfil their ecological roles. Such interactions can have a harmful or beneficial impact on the hosts depending on the emergent properties of the communities, their taxonomic structure and functionality. To evaluate these features, culture independent approaches like metabarcoding have been developed and have hugely contributed to the characterization of marine microbial diversity. The present study was aimed to explore the structure and metabolic functionality of microbial communities associated to marine hosts at the Serrana Bank, a coral atoll part of the Seaflower Biosphere Reserve (Archipelago of San Andres, Old Providence and Saint Catalina, Colombia). We found a highly diverse microbial assemblage associated with the corals Siderastrea siderea, Colpophyllia natans and Orbicella annularis, the sponge Haliclona sp. and sediment from Isla de los Pajaros lagoon. However, the coral Porites astreoides had significantly lower bacterial diversity and a different community composition. Proteobacteria was the most abundant phylum within bacterial communities in the evaluated hosts, except in P. astreoides, where Cyanobacteria was the predominant group. Firmicutes, Actinobacteria, Bacteroidetes, Acidobacteria, Chloroflexi and Gemmatimonadetes were also identified within all microbiomes, but their dominance varied between hosts. Additionally, the most abundant group among the fungi communities associated with O. annularis, S. siderea and C. natans was Ascomycota, but significant differences between clasess and order were observed among hosts. Finally, functional profiles revealed that the principal microbial functions were focused on membrane transport, carbohydrates, amino acids and energy metabolism, replication and translation processes. A significant higher metabolic functionality was found in the sponge microbiome in comparison to the coral microbial communities.

Microbial photosynthetic and photoprotective pigments in Himalayan soils originating from different elevations and successional stages

Soil microbes evolved complex metabolic strategies including photoprotective and photosynthetic pigments to survive the environmental stress including high UV irradiance, oscillating temperature and drought. Despite pigment importance for survival of soil microbes in alpine ecosystems, there have been few efforts documenting the soil pigment content, diversity and the dependence on microbial soil community, soil physico-chemical properties and constraining climatic factors. We examine how the composition and content of pigments in microbial soil communities in the Himalayas differ between major habitats spread across an elevation 4300–6000 m including cold deserts, steppes, alpine and subnival vegetation, and between several primary successional stages behind retreating glaciers, in relation to soil nutrient and water availability. Scytonemin was the prominent pigment across all of the studied habitats, followed by chlorophyll a, b; myxoxanthophyll and β-carotene. Rarely documented microbial pigments were also detected, including bacteriochlorophyll a and (2S,29S)-oscillol 2,29-di(a-l-fucoside). The contents of most of the investigated pigments showed a unimodal-shape relation to the cyanobacterial biomass. Pigments also differed in elevation optima. Alpine meadow soils had more diverse microbial and pigment assemblages than desert and steppe soils, or pioneer soils developing behind retreating glaciers. Pigments also varied across primary succession, with most pigments having a mid-successional peak. The best soil chemical predictors of pigment compositional variation were total nitrogen and cation contents. Our results shed light on the pigment composition and content in soil microbial assemblages and bring new information on ecological drivers influencing the production of photoprotective and photosynthetic pigments in Himalayan soils.

High diversity of benthic bacterial and archaeal assemblages in deep-Mediterranean canyons and adjacent slopes

Submarine canyons and slopes increase the topographic heterogeneity of continental margins and enhance mass and energy transfer from the shelf to the deeper basins, profoundly influencing the biodiversity and functioning of deep-sea ecosystems. However, information on the distribution and diversity of microbial assemblages in such habitats is extremely scant. In the present study, for the first time, we investigated abundances of benthic prokaryotes and their diversity (i.e., bacterial and archaeal) in two of the largest canyons of the Mediterranean Sea (Bisagno and Polcevera Canyons, in the Ligurian Margin) and their adjacent open slope along a water-depth gradient from 200 to 2000 m. We found that prokaryotic abundance and the richness of Operational Taxonomic Units (OTUs) varied within a narrow range despite the high variability of thermohaline and trophic conditions in the habitats investigated. Conversely, the taxonomic composition (in terms of OTUs) was highly variable among the different habitats and depths investigated. The largest fraction of OTUs (representing >80% of the total OTUs identified) were unique of each sampling site, indicating a high prokaryotic β-diversity among the investigated systems. Thermo-haline and trophic conditions and water depth only partially influenced the composition of the prokaryotic assemblages suggesting that other factors, potentially related to physical forcing typically occurring in margin ecosystems, could promote a high diversification of benthic bacterial and archaeal assemblages. This study provides new insights into the benthic prokaryotic diversity of Ligurian canyons and suggests that microbial assemblages thriving in continental margins can largely contribute to the whole diversity of Mediterranean deep-sea ecosystems.

Defunct gold mine tailings are natural reservoir for unique bacterial communities revealed by high-throughput sequencing analysis

Mine tailing dumps are arguably one of the leading sources of environmental degradation with often both public health and ecologically consequences. The present study investigated the concentration of heavy metals in gold mine tailings, and used high throughput sequencing techniques to determine the microbial community diversity of these tailings using 16S rRNA gene based amplicon sequence analysis. The concentration of detected metals and metalloids followed the order Si > Al > Fe > K > Ca > Mg. The 16S rRNA gene based sequence analysis resulted in a total of 273,398 reads across the five samples, represented among 7 major phyla, 41 classes, 77 orders, 142 families and 247 major genera. Phylum Actinobacteria was the most dominant, followed by Proteobacteria, Firmicutes, Chloroflexi, Cyanobacteria, Bacteroidetes, Acidobacteria and Planctomycetes. Redundancy analysis (RDA) and pairwise correlation analysis positively correlated the distribution of Alphaproteobacteria and Gammaproteobacteria to Al and K; Actinobacteria to Cr and Chloroflexi to Si. Negative correlations were observed in the distribution of Bacteroidetes with respect to As concentrations, Actinobacteria to Al, and Alphaproteobacteria and Gammaproteobacteria to high As and Te content of the soils. Predictive functional analysis showed the presence of putative biosynthetic and degradative pathways across the five sample sites. The study concludes that mine tailing sites harbour diverse and unique microbial assemblages with potentially biotechnologically important genes for biosynthesis and biodegradation.

Editorial special issue: the soil, the seed, the microbes and the plant

Introduction Despite the long-held belief that reproductive and disseminative organs of plants are sterile, it is now well established that seeds host diverse microbial assemblages (Hardoim et al. 2015; Truyens et al. 2015). Some of these associated microorganisms contribute to plant health, plant growth, and seed survival while others are detrimental (Barret et al. 2016; Saikkonen et al. 2016). Seeds can facilitate the dispersal of microorganisms, providing for early colonization of a new plant generation. Although seeds are an important means of supporting microbial growth and dispersal, relatively little is known about the ecology of seed-associated microorganisms (Saikkonen et al. 1998; Compant et al. 2010; Truyens et al. 2015; Brader et al. 2017) in comparison with root- and leaf-associated microorganisms (Mercado-Blanco and Lugtenberg 2014; Mercado-Blanco 2015; Vacher et al. 2016; Compant et al. 2016). In many instances, the composition and structure of the seed microbiota of various plants species have yet to be characterized. This includes the microorganisms living on the surface as well as the inner tissues of the seeds. Furthermore, a thorough understanding of the specific routes of seed transmission of microorganisms needs to be developed. Whereas seed transmission has been thought to occur through three main routes: the internal, floral and external pathways (Maude 1996), the relative importance of these pathways in determining the composition of the seed microbiota remains to be explored. Moreover, the impact of vertical (derived from the mother plant) and horizontal transmission (derived from air-borne or soil-borne microorganisms) in the assembly of seed microbial communities is unclear for some taxa. As much needs to be understood about seed-associated microbes, perhaps among the most important are resolving the relative roles of horizontal and vertical transmission in establishing the seed microbiota, which could lead to a better understanding of the plant holobiont, its microbiome and functioning, and the potential use of seed-associated microbes for improving agricultural productivity. This understanding could like lead to insights into the evolution of specific microbial taxa within seeds and the relative contributions of various selective forces in shaping the seed microbiota. The unraveling of these processes could provide important knowledge about how beneficial, commensal, and pathogenic fungal and bacterial microorganisms establish and maintain intimate associations with their seeds and contribute to the health of the next plant generation, improving our abilities to develop successful application strategies for microbial inoculants and their integration into sustainable crop production and protection. Since the nineteenth century, advances have been made in our understanding of plant-associated microorganisms. However, for seeds and their microbiota, there remain large gaps in our knowledge. Seed transmission of some microorganisms like Epichloids in grasses (Kauppinen et al. 2016; Saikkonen et al. 2016) or phytopathogenic fungi and bacteria (Li et al. 2017; Brader et al. 2017) have been relatively well studied. However, seed transmission of many plant-associated microorganisms remains unknown. The contributions in this Special Issue have served to greatly improve our understanding of the mechanisms of seed-microbe-soil interactions, the nature of the microbiota and functioning of the microbiome present within various seeds, the evolution of the seed microbiota, and the routes of microbial colonization. The studies include different beneficial and detrimental microorganisms as fungi and bacteria thriving as endophytes in different kinds of plants. They further describe ways in which specific native or non-native seed microorganisms may be utilized for improving seed and seedling survival and plant health and productivity

Microplastic-associated bacterial assemblages in the intertidal zone of the Yangtze Estuary

Plastic trash is common in oceans. Terrestrial and marine ecosystem interactions occur in the intertidal zone where accumulation of plastic frequently occurs. However, knowledge of the plastic-associated microbial community (the plastisphere) in the intertidal zone is scanty. We used high-throughput sequencing to profile the bacterial communities attached to microplastic samples from intertidal locations around the Yangtze estuary in China. The structure and composition of plastisphere communities varied significantly among the locations. We found the taxonomic composition on microplastic samples was related to their sedimentary and aquatic origins. Correlation network analysis was used to identify keystone bacterial genera (e.g. Rhodobacterales, Sphingomonadales and Rhizobiales), which represented important microbial associations within the plastisphere community. Other species (i.e. potential pathogens) were considered as hitchhikers in the plastic attached microbial communities. Metabolic pathway analysis suggested adaptations of these bacterial assemblages to the plastic surface-colonization lifestyle. These adaptations included reduced “cell motility” and greater “xenobiotics biodegradation and metabolism.” The findings illustrate the diverse microbial assemblages that occur on microplastic and increase our understanding of plastisphere ecology.

Introduced ascidians harbor highly diverse and host-specific symbiotic microbial assemblages

Many ascidian species have experienced worldwide introductions, exhibiting remarkable success in crossing geographic borders and adapting to local environmental conditions. To investigate the potential role of microbial symbionts in these introductions, we examined the microbial communities of three ascidian species common in North Carolina harbors. Replicate samples of the globally introduced species Distaplia bermudensis, Polyandrocarpa anguinea, and P. zorritensis (n = 5), and ambient seawater (n = 4), were collected in Wrightsville Beach, NC. Microbial communities were characterized by next-generation (Illumina) sequencing of partial (V4) 16S rRNA gene sequences. Ascidians hosted diverse symbiont communities, consisting of 5,696 unique microbial OTUs (at 97% sequenced identity) from 44 bacterial and three archaeal phyla. Permutational multivariate analyses of variance revealed clear differentiation of ascidian symbionts compared to seawater bacterioplankton, and distinct microbial communities inhabiting each ascidian species. 103 universal core OTUs (present in all ascidian replicates) were identified, including taxa previously described in marine invertebrate microbiomes with possible links to ammonia-oxidization, denitrification, pathogenesis, and heavy-metal processing. These results suggest ascidian microbial symbionts exhibit a high degree of host-specificity, forming intimate associations that may contribute to host adaptation to new environments via expanded tolerance thresholds and enhanced holobiont function.

Within gut physicochemical variation does not correspond to distinct resident fungal and bacterial communities in the tree-killing xylophage, Anoplophora glabripennis

Insect guts harbor diverse microbial assemblages that can be influenced by multiple factors, including gut physiology and interactions by the host with its environment. The Asian longhorned beetle (A. glabripennis; Cerambycidae: Lamiinae) is an invasive tree–killing insect that harbors a diverse consortium of fungal and bacterial gut associates that provision nutrients and facilitate lignocellulose digestion. The physicochemical conditions of the A. glabripennis gut and how these conditions may influence the microbial composition across gut regions are unknown. In this study, we used microsensors to measure in situ oxygen concentrations, pH, and redox potential along the length of the A. glabripennis larval gut from two North American populations. We then analyzed and compared bacterial and fungal gut communities of A. glabripennis within individual hosts along the length of the gut using 16S and ITS1 amplicon sequencing. The A. glabripennis midgut lumen was relatively anoxic (<0.01kPa) with a pH gradient from 5.5 to 9, moving anterior to posterior. Redox potential was higher in the anterior midgut relative to posterior regions. No differences in physicochemistry were measured between the two populations of the beetle, but the two populations harbored different communities of bacteria and fungi. However, microbial composition of the A. glabripennis gut microbiota did not differ among gut regions despite physicochemical differences. Unlike other insect systems that have distinct gut compartmentalization and corresponding microbial assemblages, the A. glabripennis gut lacks dramatic morphological modifications, which may explain why discrete microbial community structures were not found along the digestive system.

Skin microbiota differs drastically between co-occurring frogs and newts.

Diverse microbial assemblages inhabit amphibian skin and are known to differ among species; however, few studies have analysed these differences in systems that minimize confounding factors, such as season, location or host ecology. We used high-throughput amplicon sequencing to compare cutaneous microbiotas among two ranid frogs (Rana dalmatina, R. temporaria) and four salamandrid newts (Ichthyosaura alpestris, Lissotriton helveticus, L. vulgaris, Triturus cristatus) breeding simultaneously in two ponds near Braunschweig, Germany. We found that bacterial communities differed strongly and consistently between these two distinct amphibian clades. While frogs and newts had similar cutaneous bacterial richness, their bacterial composition strongly differed. Average Jaccard distances between frogs and newts were over 0.5, while between species within these groups distances were only 0.387 and 0.407 for frogs and newts, respectively. At the operational taxonomic unit (OTU) level, 31 taxa exhibited significantly different relative abundances between frogs and newts. This finding suggests that chemical or physical characteristics of these amphibians' mucosal environments provide highly selective conditions for bacterial colonizers. Multi-omics analyses of hosts and their microbiota as well as directed efforts to understand chemical differences in the mucosal environments (e.g. pH), and the specificities of host-produced compounds against potential colonizers will help to better understand this intriguing pattern.

Genetic diversity associated with N-cycle pathways in microbialites from Lake Alchichica, Mexico

Author(s): Alcantara-Hernandez, RJ; Valdespino-Castillo, PM; Centeno, CM; Alcocer, J; Merino-Ibarra, M; Falcon, LI | Abstract: Microbialites are an example of complex and diverse microbial assemblages where several metabolic pathways are interconnected for biomass formation coupled to mineral precipitation. Lake Alchichica (Mexico) is an oligotrophic environment where nitrogen (N) and phosphorus alternately limit productivity, and massive microbialite growths are found along the lake's perimeter. Previous studies have described the importance of N2 fixation in these microbialites, although other pathways associated with the N cycle, including denitrification, nitrification and anaerobic ammonium oxidation (anammox), had not been evaluated. This study identified the genetic diversity associated with N cycling in both metagenomic DNA and RNA expression by targeting key genes for nitrogenase (nifH), ammonia monooxygenase (amoA), nitrite oxidoreductase (nxrA, nxrB), hydrazine oxidoreductase (hzo) and nitrite (nirS and nirK) and nitrous oxide (nosZ) reductases. While the genetic potential for N2 fixation, ammonia oxidation, anammox and denitrification was present in the microbialites of Lake Alchichica, the most transcribed pathway was N2 fixation.

Compartmentalization of microbial communities that inhabit the hindguts of millipedes

The gut lumen of the arthropod detritivore provides hospitable and multifaceted environments for diverse assemblages of microbes. Many microbes, including trichomycetes fungi, bacteria, and archaea establish stable, adherent communities on the cuticular surface secreted by the hindgut epithelium. Regional differences in the surface topography within the hindgut of a given millipede are reflected in differing and diverse microbial assemblages. The spirostreptid millipede Cambala speobia is a detritivore found on the floors of Texas caves. This millipede species has a very circumscribed distribution in North America and a diet confined to the limited litter that accumulates on floors of these caves while the common julid millipede Cylindroiulus caeruleocinctus, an introduced European species, feeds on the diverse litter found in organic soils throughout North America. In both millipedes, the gut lumina are inhabited along their entire lengths by microbes, with the highest microbial densities in the hindguts. The anterior third of the hindgut with its distinctive six-fold symmetry is lined by cuticle having fine polarized scales, and the posterior-most third is lined by smooth cuticle. Trichomycetes only inhabit the anterior third of the hindgut, and scattered patches of filamentous bacteria along with their smaller adherent microbes occupy the posterior third. The densest populations of microbes inhabit the central region of the hindgut. Over the cuticular surface of this hindgut region, uniformly distributed indentations mark possible channels for nutrient and water exchange between the hindgut lumen and host hemolymph. Films of microbes are adherent to the cuticle that lines the hindgut while those microbes in the remainder of the gut (i.e., foregut + midgut) represent mostly unattached inhabitants.

Characterization of microbial associations with methanotrophic archaea and sulfate-reducing bacteria through statistical comparison of nested Magneto-FISH enrichments.

Methane seep systems along continental margins host diverse and dynamic microbial assemblages, sustained in large part through the microbially mediated process of sulfate-coupled Anaerobic Oxidation of Methane (AOM). This methanotrophic metabolism has been linked to consortia of anaerobic methane-oxidizing archaea (ANME) and sulfate-reducing bacteria (SRB). These two groups are the focus of numerous studies; however, less is known about the wide diversity of other seep associated microorganisms. We selected a hierarchical set of FISH probes targeting a range of Deltaproteobacteria diversity. Using the Magneto-FISH enrichment technique, we then magnetically captured CARD-FISH hybridized cells and their physically associated microorganisms from a methane seep sediment incubation. DNA from nested Magneto-FISH experiments was analyzed using Illumina tag 16S rRNA gene sequencing (iTag). Enrichment success and potential bias with iTag was evaluated in the context of full-length 16S rRNA gene clone libraries, CARD-FISH, functional gene clone libraries, and iTag mock communities. We determined commonly used Earth Microbiome Project (EMP) iTAG primers introduced bias in some common methane seep microbial taxa that reduced the ability to directly compare OTU relative abundances within a sample, but comparison of relative abundances between samples (in nearly all cases) and whole community-based analyses were robust. The iTag dataset was subjected to statistical co-occurrence measures of the most abundant OTUs to determine which taxa in this dataset were most correlated across all samples. Many non-canonical microbial partnerships were statistically significant in our co-occurrence network analysis, most of which were not recovered with conventional clone library sequencing, demonstrating the utility of combining Magneto-FISH and iTag sequencing methods for hypothesis generation of associations within complex microbial communities. Network analysis pointed to many co-occurrences containing putatively heterotrophic, candidate phyla such as OD1, Atribacteria, MBG-B, and Hyd24-12 and the potential for complex sulfur cycling involving Epsilon-, Delta-, and Gammaproteobacteria in methane seep ecosystems.

Coral-Associated Bacterial Diversity Is Conserved across Two Deep-Sea Anthothela Species.

Cold-water corals, similar to tropical corals, contain diverse and complex microbial assemblages. These bacteria provide essential biological functions within coral holobionts, facilitating increased nutrient utilization and production of antimicrobial compounds. To date, few cold-water octocoral species have been analyzed to explore the diversity and abundance of their microbial associates. For this study, 23 samples of the family Anthothelidae were collected from Norfolk (n = 12) and Baltimore Canyons (n = 11) from the western Atlantic in August 2012 and May 2013. Genetic testing found that these samples comprised two Anthothela species (Anthothela grandiflora and Anthothela sp.) and Alcyonium grandiflorum. DNA was extracted and sequenced with primers targeting the V4–V5 variable region of the 16S rRNA gene using 454 pyrosequencing with GS FLX Titanium chemistry. Results demonstrated that the coral host was the primary driver of bacterial community composition. Al. grandiflorum, dominated by Alteromonadales and Pirellulales had much higher species richness, and a distinct bacterial community compared to Anthothela samples. Anthothela species (A. grandiflora and Anthothela sp.) had very similar bacterial communities, dominated by Oceanospirillales and Spirochaetes. Additional analysis of core-conserved bacteria at 90% sample coverage revealed genus level conservation across Anthothela samples. This core included unclassified Oceanospirillales, Kiloniellales, Campylobacterales, and genus Spirochaeta. Members of this core were previously recognized for their functional capabilities in nitrogen cycling and suggest the possibility of a nearly complete nitrogen cycle within Anthothela species. Overall, many of the bacterial associates identified in this study have the potential to contribute to the acquisition and cycling of nutrients within the coral holobiont.

Biogeography and Community Diversity of Epilithic Bacterial Assemblages on Monuments: Comparisons between Maya Sites

Aims: Surfaces of cultural monuments are covered with diverse surface-associated microbial assemblages as a result of the substrata such as limestone that the monuments are constructed with as well as the impacts of various environmental pressures on these perpetually exposed structures over a long period. The aim of this study was to examine and compare the epilithic microbial assemblages on two Maya (i.e. Altun Ha and Xunanthunich) sites located in Belize. Methods and results: High-throughput 454 pyrosequencing approach was utilized to elucidate microbial community assemblages on two monuments. Overall, the taxonomic composition of the epilithic assemblages on both sites revealed the numerical dominance by members of the Proteobacteria at 43% and 36.9%, and the Cyanobacteria at 25.8% and 16.6% on Altun Ha and Xunanthunich, respectively. Comparatively, sequence diversity appeared more pronounced among the epilithic assemblages found on Xunanthunich than those on Altun Ha. Conclusions: The occurrence of relatively different epilithic assemblages on the two sites is probably indicative of the variations in the impacts of weathering and other environmental pressures over a long period on both monuments. Significance and impact of study: The results obtained from this study further emphasize the ecological importance of the delineation and elucidation of the bio-geographical distribution and community diversity of epiphytic assemblages on monuments.