Characterization of microbial communities from rumen and large intestine of lactating creole goats grazing in arid plant communities

Microbiology ◽  
2021 ◽  
Vol 167 (10) ◽  
Author(s):  
Aarón Barraza ◽  
Juan J. Montes-Sánchez ◽  
M. Goretty Caamal-Chan ◽  
Abraham Loera-Muro
Keyword(s):  
Bacterial Community ◽  
Microbial Communities ◽  
Plant Communities ◽  
Large Intestine ◽  
Bacterial Communities ◽  
Sonoran Desert ◽  
Rainy Season ◽  
Native Plant ◽  
Content Type ◽  
Link Type

Arid plant communities provide variable diets that can affect digestive microbial communities of free-foraging ruminants. Thus, we used next-generation sequencing of 16S and 18S rDNA to characterize microbial communities in the rumen (regurgitated digesta) and large intestine (faeces) and diet composition of lactating creole goats from five flocks grazing in native plant communities in the Sonoran Desert in the rainy season. The bacterial communities in the rumen and large intestine of the five flocks had similar alpha diversity (Chao1, Shannon, and Simpson indices). However, bacterial community compositions were different: a bacterial community dominated by Proteobacteria in the rumen transitioned to a community dominated by Firmicutes in the large intestine. Bacterial communities of rumen were similar across flocks; similarly occurred with large-intestine communities. Archaea had a minimum presence in the goat digestive tract. We detected phylum Basidiomycota, Ascomycota, and Apicomplexa as the main fungi and protozoa. Analyses suggested different diet compositions; forbs and grasses composed the bulk of plants in the rumen and forbs and shrubs in faeces. Therefore, lactating goats consuming different diets in the Sonoran Desert in the rainy season share a similar core bacterial community in the rumen and another in the large intestine and present low archaeal communities.

scholarly journals Tagging Frogs with Passive Integrated Transponders Causes Disruption of the Cutaneous Bacterial Community and Proliferation of Opportunistic Fungi

2014 ◽  
Vol 80 (15) ◽  
pp. 4779-4784 ◽  
Author(s):  
Rachael E. Antwis ◽  
Gerardo Garcia ◽  
Andrea L. Fidgett ◽  
Richard F. Preziosi
Keyword(s):  
Bacterial Community ◽  
Microbial Communities ◽  
Bacterial Communities ◽  
Pathogenic Fungus ◽  
Fold Increase ◽  
Bacterial Strains ◽  
Opportunistic Fungi ◽  
Content Type ◽  
Pit Tagging

ABSTRACTSymbiotic bacterial communities play a key role in protecting amphibians from infectious diseases including chytridiomycosis, caused by the pathogenic fungusBatrachochytrium dendrobatidis. Events that lead to the disruption of the bacterial community may have implications for the susceptibility of amphibians to such diseases. Amphibians are often marked both in the wild and in captivity for a variety of reasons, and although existing literature indicates that marking techniques have few negative effects, the response of cutaneous microbial communities has not yet been investigated. Here we determine the effects of passive integrated transponder (PIT) tagging on culturable cutaneous microbial communities of captive Morelet's tree frogs (Agalychnis moreletii) and assess the isolated bacterial strains for anti-B. dendrobatidisactivityin vitro. We find that PIT tagging causes a major disruption to the bacterial community associated with the skin of frogs (∼12-fold increase in abundance), as well as a concurrent proliferation in resident fungi (up to ∼200-fold increase). Handling also caused a disruption the bacterial community, although to a lesser extent than PIT tagging. However, the effects of both tagging and handling were temporary, and after 2 weeks, the bacterial communities were similar to their original compositions. We also identify two bacterial strains that inhibitB. dendrobatidis, one of which increased in abundance on PIT-tagged frogs at 1 day postmarking, while the other was unaffected. These results show that PIT tagging has previously unobserved consequences for cutaneous microbial communities of frogs and may be particularly relevant for studies that intend to use PIT tagging to identify individuals involved in trials to develop probiotic treatments.

scholarly journals Ecological networks reveal contrasting patterns of bacterial and fungal communities in glacier-fed streams in Central Asia

2019 ◽  
Author(s):  
Ze Ren ◽  
Hongkai Gao
Keyword(s):  
Bacterial Community ◽  
Microbial Communities ◽  
Central Asia ◽  
Fungal Community ◽  
Bacterial Communities ◽  
Beta Diversity ◽  
Hydrological Modeling ◽  
Alpha Diversity ◽  
Environmental Variation ◽  
Fungal Communities

Bacterial and fungal communities in biofilms are important components in driving biogeochemical processes in stream ecosystems. Previous studies have well documented the patterns of bacterial alpha diversity in stream biofilms in glacier-fed streams, where, however, beta diversity of the microbial communities has received much less attention especially considering both bacterial and fungal communities. A focus on beta diversity can provide insights into the mechanisms driving community changes associated to large environmental fluctuations and disturbances, such as in glacier-fed streams. Moreover, modularity of co-occurrence networks can reveal more ecological and evolutionary properties of microbial communities beyond taxonomic groups. Here, integrating beta diversity and co-occurrence approach, we explored the network topology and modularity of the bacterial and fungal communities with consideration of environmental variation in glacier-fed streams in Central Asia. Combining results from hydrological modeling and normalized difference of vegetation index, this study highlighted that hydrological variables and vegetation status are major variables determining the environmental heterogeneity of glacier-fed streams. Bacterial communities formed a more complex and connected network, while the fungal communities formed a more clustered network. Moreover, the strong interrelations among the taxonomic dissimilarities of bacterial community and modules suggest they had common processes in driving diversity and taxonomic compositions across the heterogeneous environment. In contrast, fungal community and modules generally showed distinct driving processes to each other. Moreover, bacterial and fungal communities also had different driving processes. Furthermore, the variation of bacterial community and modules were strongly correlated with hydrological properties and vegetation status but not with nutrients, while fungal community and modules (except one module) were not associated with environmental variation. Our results suggest that bacterial and fungal communities had distinct mechanisms in structuring microbial networks, and environmental variation had strong influences on bacterial communities but not on fungal communities. The fungal communities have unique assembly mechanisms and physiological properties which might lead to their insensitive responses to environmental variations compared to bacterial communities. Overall, beyond alpha diversity in previous studies, these results add our knowledge that bacterial and fungal communities have contrasting assembly mechanisms and respond differently to environmental variation in glacier-fed streams.

scholarly journals Ecological networks reveal contrasting patterns of bacterial and fungal communities in glacier-fed streams in Central Asia

2019 ◽  
Author(s):  
Ze Ren ◽  
Hongkai Gao
Keyword(s):  
Bacterial Community ◽  
Microbial Communities ◽  
Central Asia ◽  
Fungal Community ◽  
Bacterial Communities ◽  
Beta Diversity ◽  
Hydrological Modeling ◽  
Alpha Diversity ◽  
Environmental Variation ◽  
Fungal Communities

Bacterial and fungal communities in biofilms are important components in driving biogeochemical processes in stream ecosystems. Previous studies have well documented the patterns of bacterial alpha diversity in stream biofilms in glacier-fed streams, where, however, beta diversity of the microbial communities has received much less attention especially considering both bacterial and fungal communities. A focus on beta diversity can provide insights into the mechanisms driving community changes associated to large environmental fluctuations and disturbances, such as in glacier-fed streams. Moreover, modularity of co-occurrence networks can reveal more ecological and evolutionary properties of microbial communities beyond taxonomic groups. Here, integrating beta diversity and co-occurrence approach, we explored the network topology and modularity of the bacterial and fungal communities with consideration of environmental variation in glacier-fed streams in Central Asia. Combining results from hydrological modeling and normalized difference of vegetation index, this study highlighted that hydrological variables and vegetation status are major variables determining the environmental heterogeneity of glacier-fed streams. Bacterial communities formed a more complex and connected network, while the fungal communities formed a more clustered network. Moreover, the strong interrelations among the taxonomic dissimilarities of bacterial community and modules suggest they had common processes in driving diversity and taxonomic compositions across the heterogeneous environment. In contrast, fungal community and modules generally showed distinct driving processes to each other. Moreover, bacterial and fungal communities also had different driving processes. Furthermore, the variation of bacterial community and modules were strongly correlated with hydrological properties and vegetation status but not with nutrients, while fungal community and modules (except one module) were not associated with environmental variation. Our results suggest that bacterial and fungal communities had distinct mechanisms in structuring microbial networks, and environmental variation had strong influences on bacterial communities but not on fungal communities. The fungal communities have unique assembly mechanisms and physiological properties which might lead to their insensitive responses to environmental variations compared to bacterial communities. Overall, beyond alpha diversity in previous studies, these results add our knowledge that bacterial and fungal communities have contrasting assembly mechanisms and respond differently to environmental variation in glacier-fed streams.

scholarly journals Ecological Succession of Bacterial Communities during Conventionalization of Germ-Free Mice

2012 ◽  
Vol 78 (7) ◽  
pp. 2359-2366 ◽  
Author(s):  
Merritt G. Gillilland ◽  
John R. Erb-Downward ◽  
Christine M. Bassis ◽  
Michael C. Shen ◽  
Galen B. Toews ◽  
...  
Keyword(s):  
Bacterial Community ◽  
16S Rrna ◽  
Bacterial Communities ◽  
Structural Heterogeneity ◽  
Ecological Succession ◽  
Rrna Gene ◽  
Gi Tract ◽  
Content Type ◽  
Germ Free ◽  
Over Time

ABSTRACTLittle is known about the dynamics of early ecological succession during experimental conventionalization of the gastrointestinal (GI) tract; thus, we measured changes in bacterial communities over time, at two different mucosal sites (cecum and jejunum), with germfree C57BL/6 mice as the recipients of cecal contents (input community) from a C57BL/6 donor mouse. Bacterial communities were monitored using pyrosequencing of 16S rRNA gene amplicon libraries from the cecum and jejunum and analyzed by a variety of ecological metrics. Bacterial communities, at day 1 postconventionalization, in the cecum and jejunum had lower diversity and were distinct from the input community (dominated by eitherEscherichiaorBacteroides). However, by days 7 and 21, the recipient communities had become significantly diverse and the cecal communities resembled those of the donor and donor littermates, confirming that transfer of cecal contents results in reassembly of the community in the cecum 7 to 21 days later. However, bacterial communities in the recipient jejunum displayed significant structural heterogeneity compared to each other or the donor inoculum or the donor littermates, suggesting that the bacterial community of the jejunum is more dynamic during the first 21 days of conventionalization. This report demonstrates that (i) mature input communities do not simply reassemble at mucosal sites during conventionalization (they first transform into a “pioneering” community and over time take on the appearance, in membership and structure, of the original input community) and (ii) the specific mucosal environment plays a role in shaping the community.

Sphingomonas cynarae sp. nov., a proteobacterium that produces an unusual type of sphingan

2013 ◽  
Vol 63 (Pt_1) ◽  
pp. 72-79 ◽  
Author(s):  
Adelfia Talà ◽  
Marcello Lenucci ◽  
Antonio Gaballo ◽  
Miriana Durante ◽  
Salvatore M. Tredici ◽  
...  
Keyword(s):  
Fatty Acid ◽  
16S Rrna ◽  
16S Rrna Gene ◽  
Type Species ◽  
Sensu Stricto ◽  
Rrna Gene ◽  
Globe Artichoke ◽  
Native Plant ◽  
Content Type ◽  
Link Type

Strain SPC-1T was isolated from the phyllosphere of Cynara cardunculus L. var. sylvestris (Lamk) Fiori (wild cardoon), a Mediterranean native plant considered to be the wild ancestor of the globe artichoke and cultivated cardoon. This Gram-stain-negative, catalase-positive, oxidase-negative, non-spore-forming, rod-shaped and non-motile strain secreted copious amounts of an exopolysaccharide, formed slimy, viscous, orange-pigmented colonies and grew optimally at around pH 6.0–6.5 and 26–30 °C in the presence of 0–0.5 % NaCl. Phylogenetic analysis based on comparisons of 16S rRNA gene sequences demonstrated that SPC-1T clustered together with species of the genus Sphingomonas sensu stricto. The G+C content of the DNA (66.1 mol%), the presence of Q-10 as the predominant ubiquinone, sym-homospermidine as the predominant polyamine, 2-hydroxymyristic acid (C14 : 0 2-OH) as the major hydroxylated fatty acid, the absence of 3-hydroxy fatty acids and the presence of sphingoglycolipid supported this taxonomic position. 16S rRNA gene sequence analysis showed that SPC-1T was most closely related to Sphingomonas hankookensis ODN7T, Sphingomonas insulae DS-28T and Sphingomonas panni C52T (98.19, 97.91 and 97.11 % sequence similarities, respectively). However, DNA–DNA hybridization analysis did not reveal any relatedness at the species level. Further differences were apparent in biochemical traits, and fatty acid, quinone and polyamine profiles leading us to conclude that strain SPC-1T represents a novel species of the genus Sphingomonas , for which the name Sphingomonas cynarae sp. nov. is proposed; the type strain is SPC-1T ( = JCM 17498T = ITEM 13494T). A component analysis of the exopolysaccharide suggested that it represents a novel type of sphingan containing glucose, rhamnose, mannose and galactose, while glucuronic acid, which is commonly found in sphingans, was not detected.

scholarly journals The Gut Microbiota in Camellia Weevils Are Influenced by Plant Secondary Metabolites and Contribute to Saponin Degradation

mSystems ◽  
2020 ◽  
Vol 5 (2) ◽  
Author(s):  
Shouke Zhang ◽  
Jinping Shu ◽  
Huaijun Xue ◽  
Wei Zhang ◽  
Yabo Zhang ◽  
...  
Keyword(s):  
Secondary Metabolites ◽  
Microbial Communities ◽  
Bacterial Communities ◽  
Insect Pest ◽  
Plant Secondary Metabolites ◽  
Sole Source ◽  
Chemical Defenses ◽  
Plant Interactions ◽  
Content Type ◽  
Tea Saponin

ABSTRACT The camellia weevil (CW [Curculio chinensis]) is a notorious host-specific predator of the seeds of Camellia species in China, causing seed losses of up to 60%. The weevil is capable of overcoming host tree chemical defenses, while the mechanisms of how these beetles contend with the toxic compounds are still unknown. Here, we examined the interaction between the gut microbes of CW and camellia seed chemistry and found that beetle-associated bacterial symbionts mediate tea saponin degradation. We demonstrate that the gut microbial community profile of CW was significantly plant associated, and the gut bacterial community associated with CW feeding on Camellia oleifera seeds is enriched with genes involved in tea saponin degradation compared with those feeding on Camellia sinensis and Camellia reticulata seeds. Twenty-seven bacteria from the genera Enterobacter, Serratia, Acinetobacter, and Micrococcus subsisted on tea saponin as a sole source of carbon and nitrogen, and Acinetobacter species are identified as being involved in the degradation of tea saponin. Our results provide the first metagenome of gut bacterial communities associated with a specialist insect pest of Camellia trees, and the results are consistent with a potential microbial contribution to the detoxification of tree-defensive chemicals. IMPORTANCE The gut microbiome may play an important role in insect-plant interactions mediated by plant secondary metabolites, but the microbial communities and functions of toxic plant feeders are still poorly characterized. In the present study, we provide the first metagenome of gut bacterial communities associated with a specialist weevil feeding on saponin-rich and saponin-low camellia seeds, and the results reveal the correlation between bacterial diversity and plant allelochemicals. We also used cultured microbes to establish their saponin-degradative capacity outside the insect. Our results provide new experimental context to better understand how gut microbial communities are influenced by plant secondary metabolites and how the resistance mechanisms involving microbes have evolved to deal with the chemical defenses of plants.

scholarly journals Efficient Low-pH Iron Removal by a Microbial Iron Oxide Mound Ecosystem at Scalp Level Run

2017 ◽  
Vol 83 (7) ◽  
Author(s):  
Christen L. Grettenberger ◽  
Alexandra R. Pearce ◽  
Kyle J. Bibby ◽  
Daniel S. Jones ◽  
William D. Burgos ◽  
...  
Keyword(s):  
Acid Mine Drainage ◽  
Bacterial Community ◽  
Microbial Communities ◽  
Mine Drainage ◽  
Iron Oxidation ◽  
Cost Effective ◽  
Low Ph ◽  
Content Type ◽  
Oxidation Rates ◽  
Acid Mine

ABSTRACT Acid mine drainage (AMD) is a major environmental problem affecting tens of thousands of kilometers of waterways worldwide. Passive bioremediation of AMD relies on microbial communities to oxidize and remove iron from the system; however, iron oxidation rates in AMD environments are highly variable among sites. At Scalp Level Run (Cambria County, PA), first-order iron oxidation rates are 10 times greater than at other coal-associated iron mounds in the Appalachians. We examined the bacterial community at Scalp Level Run to determine whether a unique community is responsible for the rapid iron oxidation rate. Despite strong geochemical gradients, including a >10-fold change in the concentration of ferrous iron from 57.3 mg/liter at the emergence to 2.5 mg/liter at the base of the coal tailings pile, the bacterial community composition was nearly constant with distance from the spring outflow. Scalp Level Run contains many of the same taxa present in other AMD sites, but the community is dominated by two strains of Ferrovum myxofaciens, a species that is associated with high rates of Fe(II) oxidation in laboratory studies. IMPORTANCE Acid mine drainage pollutes more than 19,300 km of rivers and streams and 72,000 ha of lakes worldwide. Remediation is frequently ineffective and costly, upwards of $100 billion globally and nearly $5 billion in Pennsylvania alone. Microbial Fe(II) oxidation is more efficient than abiotic Fe(II) oxidation at low pH (P. C. Singer and W. Stumm, Science 167:1121–1123, 1970, https://doi.org/10.1126/science.167.3921.1121 ). Therefore, AMD bioremediation could harness microbial Fe(II) oxidation to fuel more-cost-effective treatments. Advances will require a deeper understanding of the ecology of Fe(II)-oxidizing microbial communities and the factors that control their distribution and rates of Fe(II) oxidation. We investigated bacterial communities that inhabit an AMD site with rapid Fe(II) oxidation and found that they were dominated by two operational taxonomic units (OTUs) of Ferrovum myxofaciens, a taxon associated with high laboratory rates of iron oxidation. This research represents a step forward in identifying taxa that can be used to enhance cost-effective AMD bioremediation.

scholarly journals Rhizosphere Community Selection Reveals Bacteria Associated With Reduced Root Disease

2020 ◽  
Author(s):  
Chuntao Yin ◽  
Juan M. Casa Vargas ◽  
Daniel C. Schlatter ◽  
Christina H. Hagerty ◽  
Scot H. Hulbert ◽  
...  
Keyword(s):  
Bacterial Community ◽  
Plant Growth ◽  
Microbial Communities ◽  
Bacterial Communities ◽  
Wheat Root ◽  
Root Disease ◽  
Plant Diseases ◽  
16S Rrna Genes ◽  
Rrna Genes

Abstract Background: Microbes benefit plants by increasing nutrient availability, producing plant growth hormones, and protecting against pathogens. However, it is largely unknown how plants change root microbial communities. Results: In this study, we used a multi-cycle selection system and infection by the soilborne fungal pathogen Rhizoctonia solani AG8 (hereafter AG8) to examine how plants impact the rhizosphere bacterial community and recruit beneficial microorganisms to suppress soilborne fungal pathogens and promote plant growth. Successive plantings dramatically enhanced disease suppression on susceptible wheat cultivars to AG8 in the greenhouse. Accordingly, analysis of the rhizosphere soil microbial community using deep sequencing of 16S rRNA genes revealed distinct bacterial community profiles assembled over successive wheat plantings. Moreover, the cluster of bacterial communities formed from the AG8-infected rhizosphere was distinct from those without AG8 infection. Interestingly, the bacterial communities from the rhizosphere with the lowest wheat root disease gradually separated from those with the worst wheat root disease over planting cycles. Successive monocultures and application of AG8 increased the abundance of some bacterial genera which have potential antagonistic activities, such as Chitinophaga, Pseudomonas, Chryseobacterium, and Flavobacterium, and a group of plant growth-promoting (PGP) and nitrogen-fixing microbes, including Pedobacter, Variovorax, and Rhizobium. Furthermore, 47 bacteria isolates belong to 35 species were isolated. Among them, eleven and five exhibited antagonistic activities to AG8 and Rhizoctonia oryzae in vitro, respectively. Notably, Janthinobacterium displayed broad antagonism against the soilborne pathogens Pythium ultimum, AG8, and R. oryzae in vitro, and disease suppressive activity to AG8 in soil. Conclusions: Our results demonstrated that successive wheat plantings and pathogen infection can shape the rhizosphere microbial communities and specifically accumulate a group of beneficial microbes. Our findings suggest that soil community selection may offer the potential for addressing agronomic concerns associated with plant diseases and crop productivity.

Clostridium vitabionis sp. nov., isolated from the large intestine of a mini-pig

2019 ◽  
Vol 71 (3) ◽  
Author(s):  
Yeseul Shin ◽  
Jayoung Paek ◽  
Hongik Kim ◽  
Joong-Ki Kook ◽  
Young Hyo Chang
Keyword(s):  
Large Intestine ◽  
Type Species ◽  
Sequence Similarity ◽  
Diaminopimelic Acid ◽  
Minor Amount ◽  
Rrna Gene ◽  
Content Type ◽  
Link Type ◽  
Clostridium Symbiosum ◽  
A Minor

An obligately anaerobic, Gram-stain-negative, spore-forming, short rod-shaped bacterium, designated strain YH- T4B42T, was isolated from the large intestine of a mini-pig. Phylogenetic analysis based on 16S rRNA gene sequences indicated that the isolate belongs to the genus Clostridium and is most closely related to Clostridium aminophilum KCTC 5424T, Clostridium symbiosum KCTC 15329T and Clostridium butyricum KCTC 1871T, with 95.5, 92.4 and 83.0 % sequence similarity, respectively. The average nucleotide identity values for strain YH-T4B42T and the closest related strains were lower than 72 %. The G+C content of the isolate was 55.8 mol%. The cell-wall peptidoglycan was A1γ type and contained meso-diaminopimelic acid. The predominant fatty acids were C16 : 0, C18 : 1 cis 9, C14 : 0 and C18 : 0. The major end products of glucose fermentation were lactate, formate and acetate, with a minor amount of butyrate. Based on its phenotypic, phylogenetic and chemotaxonomic properties, a novel species, Clostridium vitabionis sp. nov., is proposed for strain YH-T4B42T (=KCTC 25105T=NBRC 114767T).

scholarly journals Bacteria as Emerging Indicators of Soil Condition

2016 ◽  
Vol 83 (1) ◽  
Author(s):  
Syrie M. Hermans ◽  
Hannah L. Buckley ◽  
Bradley S. Case ◽  
Fiona Curran-Cournane ◽  
Matthew Taylor ◽  
...  
Keyword(s):  
Land Use ◽  
Bacterial Community ◽  
Community Composition ◽  
Bacterial Communities ◽  
Soil Condition ◽  
Soil Types ◽  
Anthropogenic Activity ◽  
Content Type ◽  
Soil Ecosystems ◽  
The Impact

ABSTRACT Bacterial communities are important for the health and productivity of soil ecosystems and have great potential as novel indicators of environmental perturbations. To assess how they are affected by anthropogenic activity and to determine their ability to provide alternative metrics of environmental health, we sought to define which soil variables bacteria respond to across multiple soil types and land uses. We determined, through 16S rRNA gene amplicon sequencing, the composition of bacterial communities in soil samples from 110 natural or human-impacted sites, located up to 300 km apart. Overall, soil bacterial communities varied more in response to changing soil environments than in response to changes in climate or increasing geographic distance. We identified strong correlations between the relative abundances of members of Pirellulaceae and soil pH, members of Gaiellaceae and carbon-to-nitrogen ratios, members of Bradyrhizobium and the levels of Olsen P (a measure of plant available phosphorus), and members of Chitinophagaceae and aluminum concentrations. These relationships between specific soil attributes and individual soil taxa not only highlight ecological characteristics of these organisms but also demonstrate the ability of key bacterial taxonomic groups to reflect the impact of specific anthropogenic activities, even in comparisons of samples across large geographic areas and diverse soil types. Overall, we provide strong evidence that there is scope to use relative taxon abundances as biological indicators of soil condition. IMPORTANCE The impact of land use change and management on soil microbial community composition remains poorly understood. Therefore, we explored the relationship between a wide range of soil factors and soil bacterial community composition. We included variables related to anthropogenic activity and collected samples across a large spatial scale to interrogate the complex relationships between various bacterial community attributes and soil condition. We provide evidence of strong relationships between individual taxa and specific soil attributes even across large spatial scales and soil and land use types. Collectively, we were able to demonstrate the largely untapped potential of microorganisms to indicate the condition of soil and thereby influence the way that we monitor the effects of anthropogenic activity on soil ecosystems into the future.

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