Skin microbiome correlates with bioclimate and Batrachochytrium dendrobatidis infection intensity in Brazil’s Atlantic Forest treefrogs

AbstractIn Brazil’s Atlantic Forest (AF) biodiversity conservation is of key importance since the fungal pathogen Batrachochytrium dendrobatidis (Bd) has led to the rapid loss of amphibian populations here and worldwide. The impact of Bd on amphibians is determined by the host's immune system, of which the skin microbiome is a critical component. The richness and diversity of such cutaneous bacterial communities are known to be shaped by abiotic factors which thus may indirectly modulate host susceptibility to Bd. This study aimed to contribute to understanding the environment-host–pathogen interaction determining skin bacterial communities in 819 treefrogs (Anura: Hylidae and Phyllomedusidae) from 71 species sampled across the AF. We investigated whether abiotic factors influence the bacterial community richness and structure on the amphibian skin. We further tested for an association between skin bacterial community structure and Bd co-occurrence. Our data revealed that temperature, precipitation, and elevation consistently correlate with richness and diversity of the skin microbiome and also predict Bd infection status. Surprisingly, our data suggest a weak but significant positive correlation of Bd infection intensity and bacterial richness. We highlight the prospect of future experimental studies on the impact of changing environmental conditions associated with global change on environment-host–pathogen interactions in the AF.

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The leaf bacterial microbiota of female and male kiwifruit plants in distinct seasons: assessing the impact of Pseudomonas syringae pv. actinidiae

Phytobiomes Journal ◽

10.1094/pbiomes-09-20-0070-r ◽

2021 ◽

Author(s):

Aitana Ares ◽

Joana Pereira ◽

Eva Garcia ◽

Joana Costa ◽

Igor Tiago

Keyword(s):

Bacterial Community ◽

Pseudomonas Syringae ◽

Relative Abundance ◽

Bacterial Communities ◽

Defense Mechanisms ◽

Abiotic Factors ◽

Illumina Miseq ◽

Rrna Gene ◽

Sequencing Platform ◽

The Impact

The pandemic Pseudomonas syringae pv. actinidiae (Psa) has been compromising the production of the kiwifruit industry in major producing countries. Abiotic factors and plant gender are known to influence the disease outcome. To better understand their impact, we have determined the diversity of the leafs bacterial communities using the V5-V6 region of the 16S rRNA gene amplicon on the Illumina MiSeq sequencing platform. Healthy and diseased female and male kiwifruit plants were analyzed in two consecutive seasons: spring and autumn. This work describes whether the season, plant gender and the presence of Psa can affect the leaves bacterial community. Fifty bacterial operational taxonomic units (OTUs) were identified and assigned to five phyla distributed by 14 different families and 23 genera. The leaves of healthy female and male kiwi plants share most of the identified bacterial populations, that undergoes major seasonal changes. In both cases a substantial increase of the relative abundance of genus Methylobacterium is observed in autumn. The presence of Psa induced profound changes on leaves bacterial communities structure translated into a reduction in the relative abundance of previously dominant genera that had been found in healthy plants, namely Hymenobacter, Sphingomonas and Massilia. The impact of Psa was less pronounced in the bacterial community structure of male plants in both seasons. Some of the naturally occurring genera have the potential to act as an antagonist or as enhancers of the defense mechanisms paving the way for environmentally friendly and sustainable disease control.

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The bacterioplankton community composition and a host genotype dependent occurrence of taxa shape the Daphnia magna gut bacterial community

FEMS Microbiology Ecology ◽

10.1093/femsec/fiaa128 ◽

2020 ◽

Vol 96 (8) ◽

Cited By ~ 1

Author(s):

Martijn Callens ◽

Luc De Meester ◽

Koenraad Muylaert ◽

Shinjini Mukherjee ◽

Ellen Decaestecker

Keyword(s):

Bacterial Community ◽

Daphnia Magna ◽

Bacterial Communities ◽

Abiotic Factors ◽

Laboratory Culture ◽

Relative Strength ◽

Major Influence ◽

Host Genotype ◽

Two Factors ◽

The Impact

ABSTRACT The assembly of host-associated bacterial communities is influenced by a multitude of biotic and abiotic factors. It is essential to gain insight in the impact and relative strength of these factors if we want to be able to predict the effects of environmental change on the assembly of host-associated bacterial communities, or deliberately modify them. The environmental pool of bacteria, from which the host is colonized, and the genetic background of the host are both considered to be important in determining the composition of host-associated bacterial communities. We experimentally assessed the relative importance of these two factors and their interaction on the composition of Daphnia magna gut bacterial communities. Bacterioplankton originating from natural ponds or a laboratory culture were used to inoculate germ-free Daphnia of different genotypes. We found that the composition of the environmental bacterial community has a major influence on the Daphnia gut bacterial community, both reflected by the presence or absence of specific taxa as well as by a correlation between abundances in the environment and on the host. Our data also indicate a consistent effect of host genotype on the occurrence of specific bacterial taxa in the gut of Daphnia over different environments.

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Bacterial communities of the rhizosphere and endorhiza associated with field-grown cucumber plants inoculated with a plant growth-promoting rhizobacterium or its genetically modified derivative

Canadian Journal of Microbiology ◽

10.1139/m97-048 ◽

1997 ◽

Vol 43 (4) ◽

pp. 344-353 ◽

Cited By ~ 48

Author(s):

W. F. Mahaffee ◽

J. W. Kloepper

Keyword(s):

Community Structure ◽

Bacterial Community ◽

Bacterial Communities ◽

Genetically Modified ◽

Acid Methyl Ester ◽

Wild Type ◽

Natural Ecosystems ◽

Genus Level ◽

Plant Growth Promoting ◽

The Impact

The future use of genetically modified microorganisms in the environment will be dependent on the ability to assess potential or theoretical risks associated with their introduction into natural ecosystems. To assess potential risks, several ecological parameters must be examined, including the impact of the introduced genetically modified organism on the microbial communities associated with the environment into which the introduction will occur. A 2-year field study was established to examine whether the indigenous bacterial communities of the rhizosphere and endorhiza (internal root tissues) were affected differently by the introduction of an unaltered wild type and its genetically modified derivative. Treatments consisted of the wild-type strain Pseudomonas fluorescens 89B-27 and a bioluminescent derivative GEM-8 (89B-27::Tn4431). Cucumber root or seed samples were taken 0, 7, 14, 21, 35, and 70 days after planting (DAP) in 1994 and 0, 7, 14, 28, 42, and 70 DAP in 1995. Samples were processed to examine the bacterial communities of both the rhizosphere and endorhiza. Over 7200 bacterial colonies were isolated from the rhizosphere and endorhiza and identified using the Sherlock System (Microbial ID, Inc.) for fatty acid methyl ester analysis. Community structure at the genus level was assessed using genera richness and Hill's diversity numbers, N1 and N2. The aerobic–heterotrophic bacterial community structure at the genus level did not significantly vary between treatments but did differ temporally. The data indicate that the introduction of the genetically modified derivative of 89B-27 did not pose a greater environmental risk than its unaltered wild type with respect to aerobic–heterotrophic bacterial community structure.Key words: diversity, ecology, PGPR, Pseudomonas, root colonizaton, GEM.

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Epidemic and endemic pathogen dynamics correspond to distinct host population microbiomes at a landscape scale

Proceedings of The Royal Society B Biological Sciences ◽

10.1098/rspb.2017.0944 ◽

2017 ◽

Vol 284 (1857) ◽

pp. 20170944 ◽

Cited By ~ 28

Author(s):

Andrea J. Jani ◽

Roland A. Knapp ◽

Cheryl J. Briggs

Keyword(s):

Infectious Disease ◽

Fungal Pathogen ◽

Batrachochytrium Dendrobatidis ◽

Infection Intensity ◽

Host Population ◽

Symbiotic Bacteria ◽

Skin Microbiome ◽

Pathogen Infection ◽

Microbiome Composition ◽

Pathogen Invasion

Infectious diseases have serious impacts on human and wildlife populations, but the effects of a disease can vary, even among individuals or populations of the same host species. Identifying the reasons for this variation is key to understanding disease dynamics and mitigating infectious disease impacts, but disentangling cause and correlation during natural outbreaks is extremely challenging. This study aims to understand associations between symbiotic bacterial communities and an infectious disease, and examines multiple host populations before or after pathogen invasion to infer likely causal links. The results show that symbiotic bacteria are linked to fundamentally different outcomes of pathogen infection: host–pathogen coexistence (endemic infection) or host population extirpation (epidemic infection). Diversity and composition of skin-associated bacteria differed between populations of the frog, Rana sierrae , that coexist with or were extirpated by the fungal pathogen, Batrachochytrium dendrobatidis (Bd). Data from multiple populations sampled before or after pathogen invasion were used to infer cause and effect in the relationship between the fungal pathogen and symbiotic bacteria. Among host populations, variation in the composition of the skin microbiome was most strongly predicted by pathogen infection severity, even in analyses where the outcome of infection did not vary. This result suggests that pathogen infection shapes variation in the skin microbiome across host populations that coexist with or are driven to extirpation by the pathogen. By contrast, microbiome richness was largely unaffected by pathogen infection intensity, but was strongly predicted by geographical region of the host population, indicating the importance of environmental or host genetic factors in shaping microbiome richness. Thus, while both richness and composition of the microbiome differed between endemic and epidemic host populations, the underlying causes are most likely different: pathogen infection appears to shape microbiome composition, while microbiome richness was less sensitive to pathogen-induced disturbance. Because higher richness was correlated with host persistence in the presence of Bd, and richness appeared relatively stable to Bd infection, microbiome richness may contribute to disease resistance, although the latter remains to be directly tested.

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Increase in Bacterial Community Diversity in Subsurface Aquifers Receiving Livestock Wastewater Input

Applied and Environmental Microbiology ◽

10.1128/aem.66.3.956-965.2000 ◽

2000 ◽

Vol 66 (3) ◽

pp. 956-965 ◽

Cited By ~ 81

Author(s):

Jang-Cheon Cho ◽

Sang-Jong Kim

Keyword(s):

Bacterial Community ◽

Bacterial Communities ◽

Community Diversity ◽

Similarity Coefficients ◽

Livestock Wastewater ◽

Contaminated Aquifer ◽

Bacterial Community Diversity ◽

Rdna Sequences ◽

Wastewater Samples ◽

The Impact

ABSTRACT Despite intensive studies of microbial-community diversity, the questions of which kinds of microbial populations are associated with changes in community diversity have not yet been fully solved by molecular approaches. In this study, to investigate the impact of livestock wastewater on changes in the bacterial communities in groundwater, bacterial communities in subsurface aquifers were analyzed by characterizing their 16S rDNA sequences. The similarity coefficients of restriction fragment length polymorphism (RFLP) patterns of the cloned 16S ribosomal DNAs showed that the bacterial communities in livestock wastewater samples were more closely related to those in contaminated aquifer samples. In addition, calculations of community diversity clearly showed that bacterial communities in the livestock wastewater and the contaminated aquifer were much more diverse than those in the uncontaminated aquifer. Thus, the increase in bacterial-community diversity in the contaminated aquifer was assumed to be due to the infiltration of livestock wastewater, containing high concentrations of diverse microbial flora, into the aquifer. Phylogenetic analysis of the sequences from a subset of the RFLP patterns showed that the Cytophaga-Flexibacter-Bacteroidesand low-G+C gram-positive groups originating from livestock wastewater were responsible for the change in the bacterial community in groundwater. This was evidenced by the occurrence of rumen-related sequences not only in the livestock wastewater samples but also in the contaminated-groundwater samples. Rumen-related sequences, therefore, can be used as indicator sequences for fecal contamination of groundwater, particularly from livestock.

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Effects of shade stress on morphophysiology and rhizosphere soil bacterial communities of two contrasting shade-tolerant turfgrasses

10.21203/rs.2.16025/v1 ◽

2019 ◽

Author(s):

Juanjuan Fu ◽

Yilan Luo ◽

Pengyue Sun ◽

Jinzhu Gao ◽

Donghao Zhao ◽

...

Keyword(s):

Bacterial Community ◽

Plant Growth ◽

Bacterial Communities ◽

Shade Tolerance ◽

Rhizosphere Soil ◽

Photosynthetic Capacity ◽

Bacterial Community Composition ◽

Soil Microbial Communities ◽

Soil Bacterial ◽

The Impact

Abstract Background: Shade presents one of the major abiotic limitations for turfgrass growth. Shade influences plant growth and alters plant metabolism, yet little is known about how shade affects the structure of rhizosphere soil microbial communities and the role of soil microorganisms in plant shade responses. In this study, a glasshouse experiment was conducted to examine the impact of shade stress on the growth and photosynthetic capacity of two contrasting shade-tolerant turfgrasses, shade-tolerant dwarf lilyturf (Ophiopogon japonicus, OJ) and shade-intolerant perennial turf-type ryegrass (Lolium perenne, LP). We also examined soil-plant feedback effects on shade tolerance in the two turfgrass genotypes. Bacterial community composition was assayed using high-throughput sequencing. Results: Our physiochemical data showed that under shade stress, OJ maintained higher photosynthetic capacity and root growth, thus OJ was found to be more shade-tolerant than LP. Shade-intolerant LP responded better to both shade and soil microbes than shade-tolerant OJ. Shade and live soil decreased LP growth but increased biomass allocation to shoots in the live soil. The plant shade response index of LP is higher in the live soil than sterile soil, driven by weakened soil-plant feedback under shade stress. In contrast, there was no difference in these values for OJ under similar shade and soil treatments. Illumina sequencing data revealed that shade stress had little impact on the diversity of the OJ and LP’s bacterial communities, but instead impacted the composition of bacterial communities. The bacterial communities were mostly composed of Proteobacteria and Acidobacteria in OJ soil. Further pairwise fitting analysis showed that a positive correlation of shade-tolerance in two turfgrasses and their bacterial community compositions. Several soil properties (NO3--N, NH4+-N, AK) showed a tight coupling with several major bacterial communities under shade stress, indicating that they are important drivers determining bacterial community structures. Moreover, OJ shared core bacterial taxa known to promote plant growth and confer tolerance to shade stress, which suggests common principles underpinning OJ-microbe interactions. Conclusion: Plant shade tolerance is mediated by soil-plant feedback and shade-induced changes in rhizosphere soil bacterial community structure in OJ and LP plants.

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Bacteria as Emerging Indicators of Soil Condition

Applied and Environmental Microbiology ◽

10.1128/aem.02826-16 ◽

2016 ◽

Vol 83 (1) ◽

Cited By ~ 73

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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Effects of Systemic Pesticides Imidacloprid and Metalaxyl on the Phyllosphere of Pepper Plants

BioMed Research International ◽

10.1155/2013/969750 ◽

2013 ◽

Vol 2013 ◽

pp. 1-8 ◽

Cited By ~ 21

Author(s):

Constantinos Moulas ◽

Christos Petsoulas ◽

Konstantina Rousidou ◽

Chiara Perruchon ◽

Panagiotis Karas ◽

...

Keyword(s):

Microbial Community ◽

Bacterial Community ◽

Fungal Community ◽

Bacterial Communities ◽

Potential Role ◽

Plant Foliage ◽

The Impact ◽

Impact Of Pesticides ◽

Pepper Plants

Microbes inhabiting the phyllosphere of crops are exposed to pesticides applied either directly onto plant foliage or indirectly through soil. Although, phyllosphere microbiology has been rapidly evolving, little is still known regarding the impact of pesticides on the epiphytic microbial community and especially on fungi. We determined the impact of two systemic pesticides (metalaxyl and imidacloprid), applied either on foliage or through soil, on the epiphytic fungal and bacterial communities via DGGE and cloning. Both pesticides induced mild effects on the fungal and the bacterial communities. The only exception was the foliage application of imidacloprid which showed a more prominent effect on the fungal community. Cloning showed that the fungal community was dominated by putative plant pathogenic ascomycetes (Erysiphaceae andCladosporium), while a few basidiomycetes were also present. The former ribotypes were not affected by pesticides application, while selected yeasts (Cryptococcus) were stimulated by the application of imidacloprid suggesting a potential role in its degradation. A less diverse bacterial community was identified in pepper plants. Metalaxyl stimulated an Enterobacteriaceae clone which is an indication of the involvement of members of this family in fungicide degradation. Further studies will focus on the isolation of epiphytic microbes which appear to be stimulated by pesticides application.

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Impact of Virioplankton on Archaeal and Bacterial Community Richness as Assessed in Seawater Batch Cultures

Applied and Environmental Microbiology ◽

10.1128/aem.70.2.804-813.2004 ◽

2004 ◽

Vol 70 (2) ◽

pp. 804-813 ◽

Cited By ~ 75

Author(s):

Christian Winter ◽

Arjan Smit ◽

Gerhard J. Herndl ◽

Markus G. Weinbauer

Keyword(s):

Bacterial Community ◽

Bacterial Communities ◽

Rflp Analysis ◽

Rrna Gene ◽

Tropical Atlantic ◽

Viral Lysis ◽

Batch Cultures ◽

Operational Taxonomic Units ◽

The Impact

ABSTRACT During cruises in the tropical Atlantic Ocean (January to February 2000) and the southern North Sea (December 2000), experiments were conducted to monitor the impact of virioplankton on archaeal and bacterial community richness. Prokaryotic cells equivalent to 10 to 100% of the in situ abundance were inoculated into virus-free seawater, and viruses equivalent to 35 to 360% of the in situ abundance were added. Batch cultures with microwave-inactivated viruses and without viruses served as controls. The apparent richness of archaeal and bacterial communities was determined by terminal restriction fragment length polymorphism (T-RFLP) analysis of PCR-amplified 16S rRNA gene fragments. Although the estimated richness of the prokaryotic communities generally was greatly reduced within the first 24 h of incubation due to confinement, the effects of virus amendment were detected at the level of individual operational taxonomic units (OTUs) in the T-RFLP patterns of both groups, Archaea and Bacteria. One group of OTUs was detected in the control samples but was absent from the virus-treated samples. This negative response of OTUs to virus amendment probably was caused by viral lysis. Additionally, we found OTUs not responding to the amendments, and several OTUs exhibited variable responses to the addition of inactive or active viruses. Therefore, we conclude that individual members of pelagic archaeal and bacterial communities can be differently affected by the presence of virioplankton.

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Fecal Bacterial Community of Allopatric Przewalski’s Gazelles and Their Sympatric Relatives

Frontiers in Microbiology ◽

10.3389/fmicb.2021.737042 ◽

2021 ◽

Vol 12 ◽

Author(s):

Ruoshuang Liu ◽

Jianbin Shi ◽

Susanne Shultz ◽

Dongsheng Guo ◽

Dingzhen Liu

Keyword(s):

Bacterial Community ◽

Community Composition ◽

Bacterial Communities ◽

Bacterial Community Composition ◽

Ecological Factors ◽

Ovis Aries ◽

Host Community ◽

Tibetan Sheep ◽

Fecal Bacterial Community ◽

The Impact

Mammal gastrointestinal tracts harbor diverse bacterial communities that play important roles in digestion, development, behavior, and immune function. Although, there is an increasing understanding of the factors that affect microbial community composition in laboratory populations, the impact of environment and host community composition on microbiomes in wild populations is less understood. Given that the composition of bacterial communities can be shaped by ecological factors, particularly exposure to the microbiome of other individuals, inter-specific interactions should impact on microbiome community composition. Here, we evaluated inter-population and inter-specific similarity in the fecal microbiota of Przewalski’s gazelle (Procapra przewalskii), an endangered endemic ruminant around Qinghai Lake in China. We compared the fecal bacterial communities of three Przewalski’s gazelle populations, with those of two sympatric ruminants, Tibetan gazelle (Procapra picticaudata) and Tibetan sheep (Ovis aries). The fecal bacterial community richness (Chao1, ACE) did not vary across the three Przewalski’s gazelle populations, nor did the composition vary between species. In contrast, the managed Przewalski’s gazelle population had higher bacterial diversity (Shannon and Simpson) and was more similar to its sympatric Tibetan sheep in beta diversity than the wild Przewalski’s gazelle populations. These results suggest that ecological factors like host community composition or diet affect Przewalski’s gazelle’s gastrointestinal bacterial community. The role of bacterial community composition in maintaining gastrointestinal health should be assessed to improve conservation management of endangered Przewalski’s gazelle. More broadly, captive breeding and reintroduction efforts may be impeded, where captive management results in dysbiosis and introduction of pathogenic bacteria. In free ranging populations, where wildlife and livestock co-occur, infection by domestic pathogens and diseases may be an underappreciated threat to wild animals.

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