scholarly journals The bacterial communities of Alaskan mosses and their contributions to N2-fixation

Microbiome ◽  
2021 ◽  
Vol 9 (1) ◽  
Author(s):  
Hannah Holland-Moritz ◽  
Julia E. M. Stuart ◽  
Lily R. Lewis ◽  
Samantha N. Miller ◽  
Michelle C. Mack ◽  
...  
Keyword(s):  
Microbial Communities ◽  
High Latitude ◽  
Host Species ◽  
Bacterial Communities ◽  
Light Availability ◽  
Species Identity ◽  
Moss Species ◽  
Microbiome Composition ◽  
Site Characteristics ◽  
Host Identity

Abstract Background Mosses in high-latitude ecosystems harbor diverse bacterial taxa, including N2-fixers which are key contributors to nitrogen dynamics in these systems. Yet the relative importance of moss host species, and environmental factors, in structuring these microbial communities and their N2-fixing potential remains unclear. We studied 26 boreal and tundra moss species across 24 sites in Alaska, USA, from 61 to 69° N. We used cultivation-independent approaches to characterize the variation in moss-associated bacterial communities as a function of host species identity and site characteristics. We also measured N2-fixation rates via 15N2 isotopic enrichment and identified potential N2-fixing bacteria using available literature and genomic information. Results Host species identity and host evolutionary history were both highly predictive of moss microbiome composition, highlighting strong phylogenetic coherence in these microbial communities. Although less important, light availability and temperature also influenced composition of the moss microbiome. Finally, we identified putative N2-fixing bacteria specific to some moss hosts, including potential N2-fixing bacteria outside well-studied cyanobacterial clades. Conclusions The strong effect of host identity on moss-associated bacterial communities demonstrates mosses’ utility for understanding plant-microbe interactions in non-leguminous systems. Our work also highlights the likely importance of novel bacterial taxa to N2-fixation in high-latitude ecosystems.

scholarly journals Tree Leaf Bacterial Community Structure and Diversity Differ along a Gradient of Urban Intensity

mSystems ◽  
2017 ◽  
Vol 2 (6) ◽  
Author(s):  
Isabelle Laforest-Lapointe ◽  
Christian Messier ◽  
Steven W. Kembel
Keyword(s):  
Community Structure ◽  
Bacterial Community ◽  
Microbial Communities ◽  
Human Activity ◽  
Host Species ◽  
Bacterial Communities ◽  
Urban Environments ◽  
Anthropogenic Pressures ◽  
Species Identity ◽  
Tree Leaf

ABSTRACT In natural forests, tree leaf surfaces host diverse bacterial communities whose structure and composition are primarily driven by host species identity. Tree leaf bacterial diversity has also been shown to influence tree community productivity, a key function of terrestrial ecosystems. However, most urban microbiome studies have focused on the built environment, improving our understanding of indoor microbial communities but leaving much to be understood, especially in the nonbuilt microbiome. Here, we provide the first multiple-species comparison of tree phyllosphere bacterial structures and diversity along a gradient of urban intensity. We demonstrate that urban trees possess characteristic bacterial communities that differ from those seen with trees in nonurban environments, with microbial community structure on trees influenced by host species identity but also by the gradient of urban intensity and by the degree of isolation from other trees. Our results suggest that feedback between human activity and plant microbiomes could shape urban microbiomes. Tree leaf-associated microbiota have been studied in natural ecosystems but less so in urban settings, where anthropogenic pressures on trees could impact microbial communities and modify their interaction with their hosts. Additionally, trees act as vectors spreading bacterial cells in the air in urban environments due to the density of microbial cells on aerial plant surfaces. Characterizing tree leaf bacterial communities along an urban gradient is thus key to understand the impact of anthropogenic pressures on urban tree-bacterium interactions and on the overall urban microbiome. In this study, we aimed (i) to characterize phyllosphere bacterial communities of seven tree species in urban environments and (ii) to describe the changes in tree phyllosphere bacterial community structure and diversity along a gradient of increasing urban intensity and at two degrees of tree isolation. Our results indicate that, as anthropogenic pressures increase, urban leaf bacterial communities show a reduction in the abundance of the dominant class in the natural plant microbiome, the Alphaproteobacteria. Our work in the urban environment here reveals that the structures of leaf bacterial communities differ along the gradient of urban intensity. The diversity of phyllosphere microbial communities increases at higher urban intensity, also displaying a greater number and variety of associated indicator taxa than the low and medium urban gradient sites. In conclusion, we find that urban environments influence tree bacterial community composition, and our results suggest that feedback between human activity and plant microbiomes could shape urban microbiomes. IMPORTANCE In natural forests, tree leaf surfaces host diverse bacterial communities whose structure and composition are primarily driven by host species identity. Tree leaf bacterial diversity has also been shown to influence tree community productivity, a key function of terrestrial ecosystems. However, most urban microbiome studies have focused on the built environment, improving our understanding of indoor microbial communities but leaving much to be understood, especially in the nonbuilt microbiome. Here, we provide the first multiple-species comparison of tree phyllosphere bacterial structures and diversity along a gradient of urban intensity. We demonstrate that urban trees possess characteristic bacterial communities that differ from those seen with trees in nonurban environments, with microbial community structure on trees influenced by host species identity but also by the gradient of urban intensity and by the degree of isolation from other trees. Our results suggest that feedback between human activity and plant microbiomes could shape urban microbiomes.

scholarly journals Host species, pathogens and disease associated with divergent nasal microbial communities in tortoises

2018 ◽  
Vol 5 (10) ◽  
pp. 181068
Author(s):  
Chava L. Weitzman ◽  
Franziska C. Sandmeier ◽  
C. Richard Tracy
Keyword(s):  
Host Species ◽  
Bacterial Communities ◽  
Sonoran Desert ◽  
Bacterial Community Composition ◽  
Operational Taxonomic Unit ◽  
Nasal Discharge ◽  
Microbiome Composition ◽  
Technological Advances ◽  
Repeated Sampling ◽  
Pathogen Colonization

Diverse bacterial communities are found on every surface of macro-organisms, and they play important roles in maintaining normal physiological functions in their hosts. While the study of microbiomes has expanded with the influx of data enabled by recent technological advances, microbiome research in reptiles lags behind other organisms. We sequenced the nasal microbiomes in a sample of four North American tortoise species, and we found differing community compositions among tortoise species and sampling sites, with higher richness and diversity in Texas and Sonoran desert tortoises. Using these data, we investigated the prevalence and operational taxonomic unit (OTU) diversity of the potential pathogen Pasteurella testudinis and found it to be common, abundant and highly diverse. However, the presence of this bacterium was not associated with differences in bacterial community composition within host species. We also found that the presence of nasal discharge from tortoises at the time of sampling was associated with a decline in diversity and a change in microbiome composition, which we posit is due to the harsh epithelial environment associated with immune responses. Repeated sampling across seasons, and at different points of pathogen colonization, should contribute to our understanding of the causes and consequences of different bacterial communities in these long-lived hosts.

scholarly journals Rhizosphere bacterial community composition depends on plant diversity legacy in soil and plant species identity

2018 ◽  
Author(s):  
Marc W. Schmid ◽  
Terhi Hahl ◽  
Sofia J. van Moorsel ◽  
Cameron Wagg ◽  
Gerlinde B. De Deyn ◽  
...  
Keyword(s):  
Species Diversity ◽  
Microbial Communities ◽  
Community Composition ◽  
Plant Species ◽  
Plant Diversity ◽  
Bacterial Communities ◽  
Biodiversity Loss ◽  
Plant Species Diversity ◽  
Species Identity ◽  
Soil Biodiversity

AbstractSoil microbes are known to be involved in a number of essential ecosystem processes such as nutrient cycling, plant productivity and the maintenance of plant species diversity. However, how plant species diversity and identity affect soil microbial diversity and community composition is largely unknown. We tested whether, over the course of 11 years, distinct soil bacterial communities developed under plant monocultures and mixtures, and if over this timeframe plants with a monoculture or mixture history changed in the microbial communities they associated with. For eight species, we grew offspring of plants that had been grown for 11 years in the same monocultures or mixtures (monoculture- or mixture-type plants) in pots inoculated with microbes extracted from the monoculture and mixture soils. After five months of growth in the glasshouse, we collected rhizosphere soil from each plant and used 16S-rRNA gene sequencing to determine the community composition and diversity of the bacterial communities. Microbial community structure in the plant rhizosphere was primarily determined by soil legacy (monoculture vs. mixture soil) and by plant species identity, but not by plant legacy (monoculture- vs. mixture-type plants). In seven out of the eight plant species bacterial abundance was larger when inoculated with microbes from mixture soil. We conclude that plant diversity can strongly affect belowground community composition and diversity, feeding back to the assemblage of rhizosphere microbial communities in newly establishing plants. Thereby our work demonstrates that concerns for plant biodiversity loss are also concerns for soil biodiversity loss.

scholarly journals Host dietary specialization and neutral assembly shape gut bacterial communities of wild dragonflies

2018 ◽  
Author(s):  
Rittik Deb ◽  
Ashwin Nair ◽  
Deepa Agashe
Keyword(s):  
Bacterial Community ◽  
Microbial Communities ◽  
Host Species ◽  
Bacterial Communities ◽  
Gut Contents ◽  
Spatial And Temporal Variation ◽  
Dietary Specialization ◽  
Wild Host ◽  
Dragonfly Species

ABSTRACTHost-associated gut microbial communities can have large impacts on host ecology and evolution, and are typically shaped by host taxonomy and diet. Different host species often harbor distinct microbial communities, potentially because (1) host dietary specialization determines microbial colonization, (2) host-specific selection acts on diet-acquired microbiota, and (3) a combination of both processes. While the first possibility involves passive community structuring, the other two may arise from a functional association and should produce stable microbial communities. However, these alternatives have rarely been tested in wild host populations. We used 16S rRNA amplicon sequencing to characterize the gut bacterial communities of six dragonfly species collected across multiple seasons and locations. We found that variation in bacterial community composition was predominantly explained by sampling season and location, and secondarily by host species. To distinguish the role of host dietary specialization and host-imposed selection, we used insect-specific primers to identify prey in the gut contents of three focal dragonfly species. We found that these dragonflies – considered to be generalist predators – consumed distinct prey, with seasonal diet variation. Together, the patterns of host dietary specialization and spatial and temporal variation suggest a strong role of passive processes in shaping the gut bacterial community. Indeed, the abundance and distribution of ~76% of the bacterial community members were consistent with neutral community assembly. Our results contradict the pervasive expectation that host-imposed selection shapes gut microbial communities, and highlight the importance of joint analyses of variation in host diet and gut microbial communities of natural host populations.

scholarly journals Bacterial Communities from Extreme Environments: Vulcano Island

Diversity ◽  
2019 ◽  
Vol 11 (8) ◽  
pp. 140 ◽  
Author(s):  
Camilla Fagorzi ◽  
Sara Del Duca ◽  
Stefania Venturi ◽  
Carolina Chiellini ◽  
Giovanni Bacci ◽  
...  
Keyword(s):  
Microbial Communities ◽  
Bacterial Communities ◽  
Extreme Environments ◽  
Illumina Miseq ◽  
Fumarolic Activity ◽  
Genetic Traits ◽  
Vulcano Island ◽  
Microbiome Composition ◽  
Soil Degassing ◽  
Fossa Crater

Although volcanoes represent extreme environments for life, they harbour bacterial communities. Vulcano Island (Aeolian Islands, Sicily) presents an intense fumarolic activity and widespread soil degassing, fed by variable amounts of magmatic gases (dominant at La Fossa Crater) and hydrothermal fluids (dominant at Levante Bay). The aim of this study is to analyse the microbial communities from the different environments of Vulcano Island and to evaluate their possible correlation with the composition of the gas emissions. Microbial analyses were carried out on soils and pioneer plants from both La Fossa Crater and Levante Bay. Total DNA has been extracted from all the samples and sequenced through Illumina MiSeq platform. The analysis of microbiome composition and the gases sampled in the same sites could suggest a possible correlation between the two parameters. We can suggest that the ability of different bacterial genera/species to survive in the same area might be due to the selection of particular genetic traits allowing the survival of these microorganisms. On the other side, the finding that microbial communities inhabiting different sites exhibiting different emission profiles are similar might be explained on the basis of a possible sharing of metabolic abilities related to the gas composition.

Habitat preference of the epiphyte Tillandsia recurvata (Bromeliaceae) in a semi-desert environment in Central Mexico

2005 ◽  
Vol 83 (10) ◽  
pp. 1238-1247 ◽  
Author(s):  
Rocío Bernal ◽  
Teresa Valverde ◽  
Laura Hernández-Rosas
Keyword(s):  
Seed Germination ◽  
Host Species ◽  
Seedling Survival ◽  
Desert Environment ◽  
Species Identity ◽  
Host Preferences ◽  
Tree Canopies ◽  
Tropical America ◽  
Host Identity ◽  
Germination Experiments

Tillandsia recurvata L. is an atmospheric epiphyte that occupies tree canopies in many parts of tropical America. We investigated the host preferences of this species by analyzing its occurrence on trees in a 1-ha plot in a semi-desert environment in Mexico. Additionally, we carried out germination experiments and recorded seedling survival and growth in different microsites on the three preferred host species. Our results indicate that T. recurvata occupies the crowns of certain host species (Prosopis laevigata (Humb. & Bonpl. ex Willd.) M.C. Harms, Acacia bilimekii Macbr., and Cercidium praecox (Ruiz & Pav.) Harms) with a higher frequency than expected by chance. In addition to species identity, tree size affected the probability of being occupied: small trees were occupied with lower frequencies and with lower densities than larger ones. On the other hand, distance to the nearest colonized tree was not related to the probability of a tree being occupied. Seed germination ranged from 0% to 7.5% and did not differ among the three host species tested. However, both seed germination and seedling growth were higher in the outer and upper parts of tree crowns. Given the patchy distribution of this epiphyte, we propose this system may be viewed as a metapopulation in which patch suitability varies according to host identity and size.

Effects of Host Species Identity and Diet on the Biodiversity of the Microbiota in Puerto Rican Bats

2021 ◽  
Author(s):  
Steven J. Presley ◽  
Joerg Graf ◽  
Ahmad F. Hassan ◽  
Anna R. Sjodin ◽  
Michael R. Willig
Keyword(s):  
Puerto Rican ◽  
Host Species ◽  
Species Identity

scholarly journals A gene co-association network regulating gut microbial communities in a Duroc pig population

Microbiome ◽  
2021 ◽  
Vol 9 (1) ◽  
Author(s):  
Antonio Reverter ◽  
Maria Ballester ◽  
Pamela A. Alexandre ◽  
Emilio Mármol-Sánchez ◽  
Antoni Dalmau ◽  
...  
Keyword(s):  
Microbial Communities ◽  
Candidate Genes ◽  
Relative Abundance ◽  
Association Studies ◽  
Single Gene ◽  
Host Genome ◽  
Genome Wide Association Studies ◽  
Vaccine Response ◽  
Microbiome Composition ◽  
Host Genetic

Abstract Background Analyses of gut microbiome composition in livestock species have shown its potential to contribute to the regulation of complex phenotypes. However, little is known about the host genetic control over the gut microbial communities. In pigs, previous studies are based on classical “single-gene-single-trait” approaches and have evaluated the role of host genome controlling gut prokaryote and eukaryote communities separately. Results In order to determine the ability of the host genome to control the diversity and composition of microbial communities in healthy pigs, we undertook genome-wide association studies (GWAS) for 39 microbial phenotypes that included 2 diversity indexes, and the relative abundance of 31 bacterial and six commensal protist genera in 390 pigs genotyped for 70 K SNPs. The GWAS results were processed through a 3-step analytical pipeline comprised of (1) association weight matrix; (2) regulatory impact factor; and (3) partial correlation and information theory. The inferred gene regulatory network comprised 3561 genes (within a 5 kb distance from a relevant SNP–P < 0.05) and 738,913 connections (SNP-to-SNP co-associations). Our findings highlight the complexity and polygenic nature of the pig gut microbial ecosystem. Prominent within the network were 5 regulators, PRDM15, STAT1, ssc-mir-371, SOX9 and RUNX2 which gathered 942, 607, 588, 284 and 273 connections, respectively. PRDM15 modulates the transcription of upstream regulators of WNT and MAPK-ERK signaling to safeguard naive pluripotency and regulates the production of Th1- and Th2-type immune response. The signal transducer STAT1 has long been associated with immune processes and was recently identified as a potential regulator of vaccine response to porcine reproductive and respiratory syndrome. The list of regulators was enriched for immune-related pathways, and the list of predicted targets includes candidate genes previously reported as associated with microbiota profile in pigs, mice and human, such as SLIT3, SLC39A8, NOS1, IL1R2, DAB1, TOX3, SPP1, THSD7B, ELF2, PIANP, A2ML1, and IFNAR1. Moreover, we show the existence of host-genetic variants jointly associated with the relative abundance of butyrate producer bacteria and host performance. Conclusions Taken together, our results identified regulators, candidate genes, and mechanisms linked with microbiome modulation by the host. They further highlight the value of the proposed analytical pipeline to exploit pleiotropy and the crosstalk between bacteria and protists as significant contributors to host-microbiome interactions and identify genetic markers and candidate genes that can be incorporated in breeding program to improve host-performance and microbial traits.

scholarly journals Characterization of Ocular Surface Microbial Profiles Revealed Discrepancies between Conjunctival and Corneal Microbiota

Pathogens ◽  
2021 ◽  
Vol 10 (4) ◽  
pp. 405
Author(s):  
Anna Matysiak ◽  
Michal Kabza ◽  
Justyna A. Karolak ◽  
Marcelina M. Jaworska ◽  
Malgorzata Rydzanicz ◽  
...  
Keyword(s):  
Microbial Communities ◽  
Ocular Surface ◽  
Molecular Techniques ◽  
Corneal Tissue ◽  
Rna Seq ◽  
Microbiome Composition ◽  
Viral Sequences ◽  
Pcr Techniques ◽  
Unmapped Reads

The ocular microbiome composition has only been partially characterized. Here, we used RNA-sequencing (RNA-Seq) data to assess microbial diversity in human corneal tissue. Additionally, conjunctival swab samples were examined to characterize ocular surface microbiota. Short RNA-Seq reads, obtained from a previous transcriptome study of 50 corneal tissues, were mapped to the human reference genome GRCh38 to remove sequences of human origin. The unmapped reads were then used for taxonomic classification by comparing them with known bacterial, archaeal, and viral sequences from public databases. The components of microbial communities were identified and characterized using both conventional microbiology and polymerase chain reaction (PCR) techniques in 36 conjunctival swabs. The majority of ocular samples examined by conventional and molecular techniques showed very similar microbial taxonomic profiles, with most of the microorganisms being classified into Proteobacteria, Firmicutes, and Actinobacteria phyla. Only 50% of conjunctival samples exhibited bacterial growth. The PCR detection provided a broader overview of positive results for conjunctival materials. The RNA-Seq assessment revealed significant variability of the corneal microbial communities, including fastidious bacteria and viruses. The use of the combined techniques allowed for a comprehensive characterization of the eye microbiome’s elements, especially in aspects of microbiota diversity.

scholarly journals Biological nitrous oxide consumption in oxygenated waters of the high latitude Atlantic Ocean

2021 ◽  
Vol 2 (1) ◽  
Author(s):  
Andrew P. Rees ◽  
Ian J. Brown ◽  
Amal Jayakumar ◽  
Gennadi Lessin ◽  
Paul J. Somerfield ◽  
...  
Keyword(s):  
Nitrous Oxide ◽  
Atlantic Ocean ◽  
High Latitude ◽  
Bacterial Communities ◽  
Stratospheric Ozone ◽  
Intermediate Step ◽  
Anoxic Environments ◽  
Production And Consumption ◽  
Net Flux ◽  
Traditional Understanding

AbstractNitrous oxide (N2O) is important to the global radiative budget of the atmosphere and contributes to the depletion of stratospheric ozone. Globally the ocean represents a large net flux of N2O to the atmosphere but the direction of this flux varies regionally. Our understanding of N2O production and consumption processes in the ocean remains incomplete. Traditional understanding tells us that anaerobic denitrification, the reduction of NO3− to N2 with N2O as an intermediate step, is the sole biological means of reducing N2O, a process known to occur in anoxic environments only. Here we present experimental evidence of N2O removal under fully oxygenated conditions, coupled with observations of bacterial communities with novel, atypical gene sequences for N2O reduction. The focus of this work was on the high latitude Atlantic Ocean where we show bacterial consumption sufficient to account for oceanic N2O depletion and the occurrence of regional sinks for atmospheric N2O.

Sign in / Sign up

Export Citation Format

Share Document