Beta Diversity Of Bacterial Communities Research Articles

Bacterial Communities in Cryoconite Holes of the Adjacent Glaciers on the Tibetan Plateau

Cryoconite holes are biological hotspots on the glacier surface. Cryoconite bacterial communities are strongly spatially heterogeneous at the regional scale which is closely associated with environmental variables and geographic distance. However, knowledge about the distribution patterns of cryoconite bacterial communities at a small scale and the underlying drivers is still limited. Here, we investigated bacterial communities in cryoconite holes of two adjacent glaciers of Tangula mountain range, DKMD (Dongkemadi) and LXZLB (Longxiazailongba) glacier, on the Tibetan Plateau using amplicon sequencing of the 16S rRNA gene. Cryoconite bacteria on the two glaciers have similar alpha diversity, but significantly different community compositions. Geospatial factors were the most important drivers (24.0% of the community variation) for predicting the cryoconite bacterial beta diversity in both glaciers. Latitude was the primary driver of the beta diversity of bacterial communities in the DKMD glacier, while the depth of the cryoconite holes played a dominant role in the LXZLB glacier. Collectively, these results demonstrated cryoconite bacterial communities exhibited spatial heterogeneity even at the small local scale and highlighted the importance of morphological properties of cryoconite holes instructing the distribution of cryoconite bacterial communities.

Assembly processes of bacterial and fungal communities in metal(loid)s smelter soil

There are few studies on concurrent bacterial and fungal community assembly processes that govern the metal(loid)s biogeochemical cycles at smelters. Here, a systematic investigation combined geochemical characterization, co-occurrence patterns, and assembly mechanisms of bacterial and fungal communities inhabiting soils around an abandoned arsenic smelter. Acidobacteriota, Actinobacteriota, Chloroflexi, and Pseudomonadota were dominant in bacterial communities, whereas Ascomycota and Basidiomycota dominated fungal communities. The random forest model indicated the bioavailable fractions of Fe (9.58%) were the main positive factor driving the beta diversity of bacterial communities, and the total N (8.09%) was the main negative factor for fungal communities. Microbe-contaminant interactions demonstrate the positive impact of the bioavailable fractions of certain metal(loid)s on bacteria (Comamonadaceae and Rhodocyclaceae) and fungi (Meruliaceae and Pleosporaceae). The fungal co-occurrence networks exhibited more connectivity and complexity than the bacterial networks. The keystone taxa were identified in bacterial (including Diplorickettsiaceae, norank_o_Candidatus_Woesebacteria, norank_o_norank_c_AT-s3–28, norank_o_norank_c_bacteriap25, and Phycisphaeraceae) and fungal (including Biatriosporaceae, Ganodermataceae, Peniophoraceae, Phaeosphaeriaceae, Polyporaceae, Teichosporaceae, Trichomeriaceae, Wrightoporiaceae, and Xylariaceae) communities. Meanwhile, community assembly analysis revealed that deterministic processes dominated the microbial community assemblies, which were highly impacted by pH, total N, and total and bioavailable metal(loid) content. This study provides helpful information to develop bioremediation strategies for the mitigation of metal(loid)s-polluted soils.

Association between melanin deposits in gill tissue and microbiome across different hatchery reared Atlantic salmon.

To investigate the relationship between microbial community profiles and gill pathology during a production cycle of Atlantic salmon in two commercial hatcheries. Relationships between gill histology, environmental conditions, and microbiome were determined using high-throughput data, including 16S rDNA amplicon sequencing data, histopathology data, and water quality parameters. Hatchery A used riverine water and operated a mixed system of recirculation aquaculture system (RAS) and flowthrough. Hatchery B was used bore water and operated a RAS. Melanin deposits, hyperplastic, and inflammatory lesions were observed histologically in the gills. A higher prevalence of melanin deposits was detected and correlated to a change in beta diversity of bacterial communities in early time points (fingerling and parr stages). High abundance of Sphaerotilus sp.,Pseudomonas sp.,Nitrospira sp.,Exiguobacterium sp.,Deinococcus sp.,and Comamonas sp. was correlated with a high prevalence of melanin in filaments. Bacterial diversity increased as the fish cohort transitioned from RAS to flowthrough in hatchery A. Under commercial conditions, the commensal community of gill bacteria was related to melanin prevalence.

Identifying the Role of Elevation, Geography, and Species Identity in Structuring Turtle Ant (Cephalotes Latreille, 1802) Bacterial Communities.

Bacterial communities in animals are often necessary for hosts to survive, particularly for hosts with nutrient-limited diets. The composition, abundance, and richness of these bacterial communities may be shaped by host identity and external ecological factors. The turtle ants (genus Cephalotes) are predominantly herbivorous and known to rely on bacterial communities to enrich their diet. Cephalotes have a broad Neotropical distribution, with high diversity in the South American Cerrado, a geologically and biologically diverse savanna. Using 16S rRNA amplicon sequencing, we examined the bacterial communities of forty-one Cephalotes samples of sixteen different species collected from multiple locations across two sites in the Cerrado (MG, Brazil) and compared the bacterial communities according to elevation, locality, species, and species group, defined by host phylogeny. Beta diversity of bacterial communities differed with respect to all categories but particularly strongly when compared by geographic location, species, and species group. Differences seen in species and species groups can be partially explained by the high abundance of Mesorhizobium in Cephalotes pusillus and Cephalotes depressus species groups, when compared to other clades via the Analysis of Composition of Microbiome (ANCOM). Though the Cephalotes bacterial community is highly conserved, results from this study indicate that multiple external factors can affect and change bacterial community composition and abundance.

Host-Associated Bacterial Communities Vary Between Daphnia galeata Genotypes but Not by Host Genetic Distance

Host genotype may shape host-associated bacterial communities (commonly referred to as microbiomes). We sought to determine (a) whether bacterial communities vary among host genotypes in the water flea Daphnia galeata and (b) if this difference is driven by the genetic distance between host genotypes, by using D. galeata genotypes hatched from sediments of different time periods. We used 16S amplicon sequencing to profile the gut and body bacterial communities of eight D. galeata genotypes hatched from resting eggs; these were isolated from two distinct sediment layers (dating to 1989 and 2009) of a single sediment core of the lake Greifensee, and maintained in a common garden in laboratory cultures for 5 years. In general, bacterial community composition varied in both the Daphnia guts and bodies; but not between genotypes from different sediment layers. Specifically, genetic distances between host genotypes did not correlate with beta diversity of bacterial communities in Daphnia guts and bodies. Our results indicate that Daphnia bacterial community structure is to some extent determined by a host genetic component, but that genetic distances between hosts do not correlate with diverging bacterial communities.

Condensed tannins protect against aflatoxin B1-induced toxicity in Lateolabrax maculatus by restoring intestinal integrity and regulating bacterial microbiota

Condensed tannins (CT) have been shown to enhance the exogenous stress resistance of fish, whereas the protective effects of CT against damage induced by dietary aflatoxin B1 (AFB1) on the growth and health of fish have not been evaluated. A 56-day feeding trial was carried out to assess the effects of CT on alleviating dietary AFB1-induced damages in growth, antioxidant and immune response, intestinal integrity and bacterial microbiota of the Chinese sea bass (Lateolabrax maculatus). Three diets were formulated to contain 0 mg/kg of AFB1 and 0 g/kg of CT (G1), 1 mg/kg of AFB1 and 0 g/kg of CT (G2), and 1 mg/kg of AFB1 and 1 g/kg of CT (G3), respectively. Each diet was randomly assigned to three tanks with 40 fish in each tank. Fish were fed to apparent satiation twice daily. Results indicated that fish fed G2 had lower (P < 0.05) final body weight, weight gain rate, specific growth rate, feed intake, viscerosomatic index, total antioxidant capacity, superoxide dismutase, catalase, alkaline phosphatase and lysozyme, but higher (P < 0.05) malondialdehyde, diamine oxidase and lipopolysaccharide compared to those of fish fed G1 and G3. Fish fed G3 had higher (P < 0.05) villus length and intestinal tight junction protein gene expression (ZO-1, Claudin-3 and Occludin), but lower (P < 0.05) villus width than G2. Fish had similar growth performance, serum parameters and intestinal morphology between G1 and G3. In the top 10 dominant genera of intestinal microbiota, the relative abundance of Pseudomonas was higher in G2 but lower in G3 than in G1 (P < 0.05). Compared with G1, G2 and G3 had higher relative abundances of Aeromonas and Klebsiella, but lower relative abundance of Plesiomonas (P < 0.05). Dietary treatments did not alter the alpha and beta diversity of bacterial communities. In conclusion, dietary inclusion of 1 mg/kg of AFB1 reduced feed intake and decreased growth of L. maculatus. AFB1 reduced serum antioxidant capacity and immunity, increased intestinal permeability, induced intestinal damage and altered bacterial microbiota of fish. Supplementation of 1 g/kg of grape seed CT effectively protected against AFB1 toxicity by alleviating the negative impacts of dietary AFB1 exerted on fish. This study provides a rational for the application of CT in aquaculture to prevent fish from AFB1-induced damage.

Composition of Soil Viral and Bacterial Communities after Long-Term Tillage, Fertilization, and Cover Cropping Management

Soil bacterial communities are a critical component for stability and function of terrestrial ecosystems. Viruses are ubiquitous in soils and have significant impacts on the structure and functions of bacterial host communities. However, little is known about the variation of bacterial and viral communities and their connection under various land use management practices. In this study, we evaluated bacterial and viral diversity using 16s rRNA sequencing and RAPD-PCR, respectively, and estimated viral and bacterial abundances by enumeration method, and used structural equation model to reveal relationship between viruses, bacteria, and soil properties, in soils from a long-term conservation management experimental site in western Tennessee USA. Inorganic N fertilization, cover cropping, and tillage treatments showed no significant differences in bacterial alpha-diversity but significantly influenced the structure, as suggested by differences in beta-diversity of bacterial communities. Higher soil pH and water content were favorable to bacterial abundances. Cover cropping, soil water content, and bacterial abundances may explain the variation of viral abundances and community structure in soil. Structural equation modeling showed that bacterial abundances positively influenced viral abundances, and in turn virus abundances and bacterial alpha diversity affected the level of extractable dissolved organic C, which exerted a feedback effect on the structure of bacterial communities. This feedback loop suggests that viral lysates might significantly contribute to reshaping bacterial community structure and indirect influence bacterial alpha diversity. This supports the theory of the “viral shunt” in soil ecosystems. This study indicated that long-term conservation management can reshape soil bacterial and viral communities and influence their interactions in biogeochemical processes.

Genetic structure and symbiotic profile of worldwide natural populations of the Mediterranean fruit fly, Ceratitis capitata

BackgroundThe Mediterranean fruit fly, Ceratitis capitata, is a cosmopolitan agricultural pest of worldwide economic importance and a model for the development of the Sterile Insect Technique (SIT) for fruit flies of the Tephritidae family (Diptera). SIT relies on the effective mating of laboratory-reared strains and natural populations, and therefore requires an efficient mass-rearing system that will allow for the production of high-quality males. Adaptation of wild flies to an artificial laboratory environment can be accompanied by negative effects on several life history traits through changes in their genetic diversity and symbiotic communities. Such changes may lead to reduced biological quality and mating competitiveness in respect to the wild populations. Profiling wild populations can help understand, and maybe reverse, deleterious effects accompanying laboratory domestication thus providing insects that can efficiently and effectively support SIT application.ResultsIn the present study, we analyzed both the genetic structure and gut symbiotic communities of natural medfly populations of worldwide distribution, including Europe, Africa, Australia, and the Americas. The genetic structure of 408 individuals from 15 distinct populations was analyzed with a set of commonly used microsatellite markers. The symbiotic communities of a subset of 265 individuals from 11 populations were analyzed using the 16S rRNA gene-based amplicon sequencing of single individuals (adults). Genetic differentiation was detected among geographically distant populations while adults originated from neighboring areas were genetically closer. Alpha and beta diversity of bacterial communities pointed to an overall reduced symbiotic diversity and the influence of the geographic location on the bacterial profile.ConclusionsOur analysis revealed differences both in the genetic profile and the structure of gut symbiotic communities of medfly natural populations. The genetic analysis expanded our knowledge to populations not analyzed before and our results were in accordance with the existing scenarios regarding this species expansion and colonization pathways. At the same time, the bacterial communities from different natural medfly populations have been characterized, thus broadening our knowledge on the microbiota of the species across its range. Genetic and symbiotic differences between natural and laboratory populations must be considered when designing AW-IPM approaches with a SIT component, since they may impact mating compatibility and mating competitiveness of the laboratory-reared males. In parallel, enrichment from wild populations and/or symbiotic supplementation could increase rearing productivity, biological quality, and mating competitiveness of SIT-important laboratory strains.

Differences in bacterial community structure between three types of biological soil crusts and soil below crusts from the Gurbantunggut Desert, China

The scarcity of knowledge on differences in the microbial assemblage between biological soil crusts (BSCs) and soil below crusts (SBCs) limits our understanding of the contribution of different layers of topsoil to desert ecosystems. This study used Illumina MiSeq sequencing to determine whether differences in bacterial communities among different types of BSCs (algae, lichen and moss dominated) are greater than those between BSCs and their corresponding underlying soils (0–5 cm) in the Gurbantunggut Desert, China. Alpha and beta diversity of bacterial communities showed that richness and diversity were greater in SBCs than in BSCs, but the absolute bacterial abundance was larger in BSCs than in soils. Differences were mainly in the phyla Cyanobacteria, Actinobacteria, Chloroflexi and Acidobacteria. Cyanobacteria were concentrated in BSCs, especially in algae‐dominated BSCs. The relative abundances of Actinobacteria, Chloroflexi and Acidobacteria in SBCs were more than twice those in BSCs, and they were also abundant in the lichen‐ and moss‐dominant crusts. The number of sample‐specific genera was larger in BSCs, but there were more shared genera among SBCs. These results, combined with the principal coordinate analysis and the predicted function profiles, showed that differences in microbial community structure and function in desert ecosystems were greatest between BSCs and the underlying soils, followed by differences among the three types of BSCs, and differences were smallest between the soils below different crusts. These differences might be closely related to the soil chemical properties, especially to pH and fertility. Our study indicated that microbial communities tended to converge in SBCs of different microhabitats.Highlights We studied bacterial community composition in different types of BSCs and SBCs. Differences in bacterial community were greatest between BSCs and SBCs. BSC components contributed to small‐scale microbial heterogeneity in SBCs. Surface soil bacterial communities were strongly stratified even at the centimetre scale from BSCs.

Environmental selection and dispersal limitation drive the assemblage of bacterial community in temperate forest soils

Environmental selection and dispersal limitation are two basic processes underlying community assembly. The relative importance of those two processes differs across scales, community identities, and community types. The processes responsible for structuring microbial communities in soil of temperate subalpine forest are poorly understood. Here, we investigated the relationship between soil bacterial community structure and environmental factors, and quantified the relative role of edaphic factors, vegetation, and spatial variables in shaping the structure of six soil bacterial communities (LpMC1, LpMC2, PwMC, PmMC, PtMC, and BMC) in five forest types including Larix principis-rupprechtii, Picea wilsonii, Picea meyeri, Pinus tabulaeformis, and Betula platyphylla in Pangquangou Nature Reserve by using PCR-DGGE technology. Our results showed that the structure and biodiversity of bacterial communities were significantly different among six communities. The biodiversity of bacterial community were higher in LpMC2 and PtMC, lowest in PmMC, and highest in LpMC1. Soil environmental factors, such as pH, soil water content, total carbon, total nitrogen, soil organic matter, available phosphorous, and soil enzymes, were significantly correlated with biodiversity and structure of soil bacterial community. The beta diversity of bacterial communities were significantly correlated with geographic distance, indicating the influence of dispersal limitation on the structure of bacterial community. The order of driving force on the structure of bacterial community was edaphic factors (0.27), spatial factor (0.19) and vegetation (0.15) in six samples. Using regional soil microbes from 10 samples around reserve as source community, results from the microcosm experiments showed that the edaphic factors were the predominant driving factors (0.35) on structure of artificial dispersal bacterial community, while the high diversity of source microbial community affected the structure of microcosm soil. In summary, at local scale, environmental selection predominantly determined the structural and biodiversity of soil bacterial communities in temperate subalpine forest, while dispersal limitation played a significant role. Such a result indicated that deterministic processes and stochastic processes played important roles in shaping the structure of soil bacterial community at local scale, with the former having the leading role. The composition of dispersal soil bacteria community was source-dependent but also modulated by local environmental selection.

Highly similar microbial communities are shared among related and trophically similar ant species

Ants dominate many terrestrial ecosystems, yet we know little about their nutritional physiology and ecology. While traditionally viewed as predators and scavengers, recent isotopic studies revealed that many dominant ant species are functional herbivores. As with other insects with nitrogen-poor diets, it is hypothesized that these ants rely on symbiotic bacteria for nutritional supplementation. In this study, we used cloning and 16S sequencing to further characterize the bacterial flora of several herbivorous ants, while also examining the beta diversity of bacterial communities within and between ant species from different trophic levels. Through estimating phylogenetic overlap between these communities, we tested the hypothesis that ecologically or phylogenetically similar groups of ants harbor similar microbial flora. Our findings reveal: (i) clear differences in bacterial communities harbored by predatory and herbivorous ants; (ii) notable similarities among communities from distantly related herbivorous ants and (iii) similar communities shared by different predatory army ant species. Focusing on one herbivorous ant tribe, the Cephalotini, we detected five major bacterial taxa that likely represent the core microbiota. Metabolic functions of bacterial relatives suggest that these microbes may play roles in fixing, recycling, or upgrading nitrogen. Overall, our findings reveal that similar microbial communities are harbored by ants from similar trophic niches and, to a greater extent, by related ants from the same colonies, species, genera, and tribes. These trends hint at coevolved histories between ants and microbes, suggesting new possibilities for roles of bacteria in the evolution of both herbivores and carnivores from the ant family Formicidae.