Plants of the fynbos biome harbour host species-specific bacterial communities

The ability to predict plant microbiome assembly will enable new bacterial-based technologies for agriculture. A major step towards this is quantifying the roles of ecological processes on community assembly. This is challenging, in part because individuals within a populations of host plants may be colonised by different assemblages of bacteria, simply because of variation in soil communities proximal to said plants. This creates uncertainty because it is difficult to estimate if the absence of a given species was a) because it was not present to colonise the plant or b) it went locally extinct from competition, predation or similar. To address this, the authors develop a mesocosm system to study bacterial communities of individual plants by replicated transplantation to a recipient host plant population, ensuring new hosts receive a homogenous species pool for colonisation. We sought to understand which factors affected the transplant and, what the main drivers of variation in the model communities were. A nested factorial design was used to investigate the transplantation of cultured or total, root or leaf associated bacterial communities from donor host species to surrogate host species. Specific metrics were developed to quantify colonisation efficiency of communities. The results show the root communities were more effectively transplanted than leaf communities, and a higher proportion of cultured communities were recovered than total communities. For root communities the strongest drivers of beta diversity was the donor host species, and for leaves it was the surrogate host species. Overall the results reveal that root, but not leaf communities are suited to this system reflecting their differing ecological drivers.

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Predictable and host‐species specific humanization of the gut microbiota in captive primates

Molecular Ecology ◽

10.1111/mec.15994 ◽

2021 ◽

Author(s):

Jennifer L. Houtz ◽

Jon G. Sanders ◽

Anthony Denice ◽

Andrew H. Moeller

Keyword(s):

Gut Microbiota ◽

Host Species ◽

Species Specific

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The dilution effect limits plasmid horizontal transmission in multispecies bacterial communities

Microbiology ◽

10.1099/mic.0.001086 ◽

2021 ◽

Vol 167 (9) ◽

Author(s):

Anastasia Kottara ◽

Laura Carrilero ◽

Ellie Harrison ◽

James P. J. Hall ◽

Michael A. Brockhurst

Keyword(s):

Host Species ◽

Bacterial Communities ◽

Horizontal Transmission ◽

Dilution Effect ◽

Infection Risk ◽

Host Cells ◽

Evolutionary Innovation ◽

Genomic Divergence ◽

Plasmid Diversity ◽

Plasmid Conjugation

By transferring ecologically important traits between species, plasmids drive genomic divergence and evolutionary innovation in their bacterial hosts. Bacterial communities are often diverse and contain multiple coexisting plasmids, but the dynamics of plasmids in multi-species communities are poorly understood. Here, we show, using experimental multi-species communities containing two plasmids, that bacterial diversity limits the horizontal transmission of plasmids due to the ‘dilution effect’; this is an epidemiological phenomenon whereby living alongside less proficient host species reduces the expected infection risk for a focal host species. In addition, plasmid horizontal transmission was also affected by plasmid diversity, such that the rate of plasmid conjugation was reduced from co-infected host cells carrying both plasmids. In diverse microbial communities, plasmid spread may be limited by the dilution effect and plasmid–plasmid interactions, reducing the rate of horizontal transmission.

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Host Species-Specific Protoplast Damaging Activity of Spore Germination Fluids of Blast Pathogen Magnaporthe grisea

Journal of Phytopathology ◽

10.1046/j.1439-0434.2002.00808.x ◽

2002 ◽

Vol 150 (10) ◽

pp. 576-578 ◽

Cited By ~ 3

Author(s):

R. Rathour ◽

B. M. Singh ◽

P. Plaha

Keyword(s):

Spore Germination ◽

Host Species ◽

Magnaporthe Grisea ◽

Species Specific

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Microbial control of host gene regulation and the evolution of host–microbiome interactions in primates

Philosophical Transactions of the Royal Society B Biological Sciences ◽

10.1098/rstb.2019.0598 ◽

2020 ◽

Vol 375 (1808) ◽

pp. 20190598 ◽

Cited By ~ 1

Author(s):

Laura Grieneisen ◽

Amanda L. Muehlbauer ◽

Ran Blekhman

Keyword(s):

Gene Expression ◽

Gene Regulation ◽

Host Species ◽

Evolutionary Dynamics ◽

Microbial Control ◽

Host Gene ◽

Primate Species ◽

Microbiome Composition ◽

Wide Range ◽

Species Specific

Recent comparative studies have found evidence consistent with the action of natural selection on gene regulation across primate species. Other recent work has shown that the microbiome can regulate host gene expression in a wide range of relevant tissues, leading to downstream effects on immunity, metabolism and other biological systems in the host. In primates, even closely related host species can have large differences in microbiome composition. One potential consequence of these differences is that host species-specific microbial traits could lead to differences in gene expression that influence primate physiology and adaptation to local environments. Here, we will discuss and integrate recent findings from primate comparative genomics and microbiome research, and explore the notion that the microbiome can influence host evolutionary dynamics by affecting gene regulation across primate host species. This article is part of the theme issue ‘The role of the microbiome in host evolution’.

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Multipartner Symbiosis across Biological Domains: Looking at the Eukaryotic Associations from a Microbial Perspective

mSystems ◽

10.1128/msystems.00148-19 ◽

2019 ◽

Vol 4 (4) ◽

Cited By ~ 2

Author(s):

Marta Turon ◽

Maria J. Uriz ◽

Daniel Martin

Keyword(s):

Bacterial Communities ◽

High Throughput Sequencing ◽

Marine Invertebrates ◽

Single Species ◽

Rrna Gene ◽

Polychaete Species ◽

Content Type ◽

Symbiotic Relationships ◽

Host Sponge ◽

Species Specific

ABSTRACTSponges establish tight associations with both micro- and macroorganisms. However, while studies on sponge microbiomes are numerous, nothing is currently known about the microbiomes of sponge-associated polychaetes and their relationships with those of their host sponges. We analyzed the bacterial communities of symbiotic polychaetes (Haplosyllisspp.) and their host sponges (Clathria reinwardti,Amphimedon paraviridis,Neofibularia hartmani, andAaptos suberitoides) to assess the influence of the sponges on the polychaete microbiomes. We identified both eukaryote partners by molecular (16S and COI genes) and morphological features, and we identified their microbial communities by high-throughput sequencing of the 16S rRNA gene (V4 region). We unravel the existence of sixHaplosyllisspecies (five likely undescribed) associated at very high densities with the study sponge species in Nha Trang Bay (central Vietnam). A single polychaete species inhabitedA. paraviridisand was different from the single species that inhabitedA. suberitoides. Conversely, two different polychaete species were found inC. reinwardtiandN. hartmani, depending on the two host locations. Regardless of the host sponge, polychaete microbiomes were species specific, which is a widespread feature in marine invertebrates. More than half of the polychaete bacteria were also found in the host sponge microbiome but at contrasting abundances. Thus, the associated polychaetes seemed to be able to select, incorporate, and enrich part of the sponge microbiome, a selection that appears to be polychaete species specific. Moreover, the bacterial diversity is similar in both eukaryotic partners, which additionally confirms the influence of food (host sponge) on the structure of the polychaete microbiome.IMPORTANCEThe symbiotic lifestyle represents a fundamental cryptic contribution to the diversity of marine ecosystems. Sponges are ideal targets to improve understanding the symbiotic relationships from evolutionary and ecological points of view, because they are the most ancient metazoans on earth, are ubiquitous in the marine benthos, and establish complex symbiosis with both prokaryotes and animals, which in turn also harbor their own bacterial communities. Here, we study the microbiomes of sponge-polychaete associations and confirm that polychaetes feed on their host sponges. The study worms select and enrich part of the sponge microbiome to shape their own species-specific bacterial communities. Moreover, worm microbiome diversity runs parallel to that of its food host sponge. Considering our results on symbiotic polychaetes and previous studies on fishes and mammals, diet appears to be an important source of bacteria for animals to shape their species-specific microbiomes.

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Host species-specific usage of the TLR4-LPS receptor complex

Innate Immunity ◽

10.1177/1753425908095957 ◽

2008 ◽

Vol 14 (4) ◽

pp. 223-231 ◽

Cited By ~ 38

Author(s):

Regina Lizundia ◽

Kay-Sara Sauter ◽

Geraldine Taylor ◽

Dirk Werling

Keyword(s):

Host Species ◽

Receptor Complex ◽

Species Specific

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

Royal Society Open Science ◽

10.1098/rsos.181068 ◽

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.

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Aquaponics using a fish farm effluent shifts bacterial communities profile in halophytes rhizosphere and endosphere

Scientific Reports ◽

10.1038/s41598-020-66093-8 ◽

2020 ◽

Vol 10 (1) ◽

Cited By ~ 1

Author(s):

Vanessa Oliveira ◽

Patrícia Martins ◽

Bruna Marques ◽

Daniel F. R. Cleary ◽

Ana I. Lillebø ◽

...

Keyword(s):

Natural Environment ◽

Bacterial Communities ◽

Denaturing Gradient Gel Electrophoresis ◽

Nutrient Loads ◽

Marine Aquaculture ◽

Aquaculture Effluents ◽

Specific Effects ◽

Salicornia Ramosissima ◽

Gradient Gel Electrophoresis ◽

Species Specific

AbstractThe intensification of marine aquaculture raises multiple sustainability issues, namely the handling of nutrient-rich effluents that can adversely impact ecosystems. As integrated multi-trophic aquaculture (IMTA) gains momentum, the use of halophyte plants to phytoremediate aquaculture effluents has received growing attention, particularly in aquaponics. It is, therefore, important to obtain a more in-depth knowledge of the microbial communities present in the root systems of these plants, both in their natural environment (sediment) and in aquaponics, in order to understand their nutrient removal potential. The present study used denaturing gradient gel electrophoresis (DGGE) and barcoded pyrosequencing to assess the bacterial community present in the endosphere and rhizosphere of three halophyte plants: Halimione portulacoides, Salicornia ramosissima and Sarcocornia perennis. Species-specific effects were recorded in the profile and diversity of the bacterial communities present in halophyte roots, with significant differences also recorded for the same halophyte species grown in contrasting environments (sediment vs. aquaponics). In aquaponics the most abundant groups belonged to the orders Rhodocyclales, Campylobacterales, Rhodobacterales and Desulfobacterales, while in the natural environment (sediment) the most abundant groups belonged to the orders Rhizobiales, Sphingomonadales and Alteromonadales. An overall enrichment in bacterial taxa involved in nutrient cycling was recorded in the roots of halophytes grown in aquaponics (such as Denitromonas, Mesorhizobium, Colwellia, Dokdonella and Arcobacter), thereby highlighting their potential to reduce the nutrient loads from aquaculture effluents.

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