Dominance of coniferous and broadleaved trees drives bacterial associations with boreal feather mosses

The composition of ecologically important moss-associated bacterial communities seems to be mainly driven by host species, but may also be shaped by environmental conditions related with tree-canopy dominance. The moss phyllosphere has been studied in coniferous forests while broadleaf forests remain understudied. To determine if host species or environmental conditions defined by tree-canopy dominance drives the bacterial diversity in the moss phyllosphere, we used 16S rRNA gene amplicon sequencing to quantify changes in bacterial communities as a function of host species (Pleurozium schreberi and Ptilium crista-castrensis) and forest type (coniferous black spruce versus deciduous broadleaf trembling aspen) in eastern Canada. Forest type, not host species, was the main factor affecting moss phyllosphere bacterial community composition, though the interaction of both variables was significant. Bacterial α-diversity was highest in spruce forests, while there was greater turnover (β-diversity) and higher γ-diversity in aspen forests. Unexpectedly, Cyanobacteria were much more relatively abundant in aspen than in spruce forests, with the bacterial family Nostocaceae (Cyanobacteria) differing the most between both forest types. Our results suggest that the increasing change in dominance from coniferous to broadleaf trees due to natural and anthropic disturbances is likely to affect the composition of moss-associated bacteria in boreal forests.

Download Full-text

Structure and Function of Bacterial Communities Emerging from Different Sources under Identical Conditions

Applied and Environmental Microbiology ◽

10.1128/aem.72.1.212-220.2006 ◽

2006 ◽

Vol 72 (1) ◽

pp. 212-220 ◽

Cited By ~ 118

Author(s):

Silke Langenheder ◽

Eva S. Lindström ◽

Lars J. Tranvik

Keyword(s):

Environmental Conditions ◽

Bacterial Communities ◽

Fragment Length Polymorphism ◽

Bacterial Community Composition ◽

Rrna Gene ◽

Polymorphism Analysis ◽

Scale Functions ◽

And Function ◽

Different Sources ◽

The 16S Rrna Gene

ABSTRACT The aim of this study was to compare two major hypotheses concerning the formation of bacterial community composition (BCC) at the local scale, i.e., whether BCC is determined by the prevailing local environmental conditions or by “metacommunity processes.” A batch culture experiment where bacteria from eight distinctly different aquatic habitats were regrown under identical conditions was performed to test to what extent similar communities develop under similar selective pressure. Differently composed communities emerged from different inoculum communities, as determined by terminal restriction fragment length polymorphism analysis of the 16S rRNA gene. There was no indication that similarity increased between communities upon growth under identical conditions compared to that for growth at the ambient sampling sites. This suggests that the history and distribution of taxa within the source communities were stronger regulating factors of BCC than the environmental conditions. Moreover, differently composed communities were different with regard to specific functions, such as enzyme activities, but maintained similar broad-scale functions, such as biomass production and respiration.

Download Full-text

Endophytic bacterial communities of oilseed rape associate with genotype-specific resistance against Verticillium longisporum

FEMS Microbiology Ecology ◽

10.1093/femsec/fiz188 ◽

2019 ◽

Vol 96 (1) ◽

Cited By ~ 1

Author(s):

Stefanie P Glaeser ◽

Iulian Gabur ◽

Hossein Haghighi ◽

Jens-Ole Bartz ◽

Peter Kämpfer ◽

...

Keyword(s):

Oilseed Rape ◽

Relative Abundance ◽

Bacterial Communities ◽

Quantitative Resistance ◽

Bacterial Community Composition ◽

Phylogenetic Group ◽

Rrna Gene ◽

Host Genotype ◽

Brassica Napus L ◽

Verticillium Longisporum

ABSTRACT Associations of endophytic bacterial community composition of oilseed rape (Brassica napus L.) with quantitative resistance against the soil-borne fungal pathogen Verticillium longisporum was assessed by 16S rRNA gene amplicon sequencing in roots and hypocotyls of four plant lines with contrasting genetic composition in regard to quantitative resistance reactions. The plant compartment was found to be the dominating driving factor for the specificity of bacterial communities in healthy plants. Furthermore, V. longisporum infection triggered a stabilization of phylogenetic group abundance in replicated samples suggesting a host genotype-specific selection. Genotype-specific associations with bacterial phylogenetic group abundance were identified by comparison of plant genotype groups (resistant versus susceptible) and treatment groups (healthy versus V. longisporum-infected) allowing dissection into constitutive and induced directional association patterns. Relative abundance of Flavobacteria, Pseudomonas, Rhizobium and Cellvibrio was associated with resistance/susceptibility. Relative abundance of Flavobacteria and Cellvibrio was increased in resistant genotypes according to their known ecological functions. In contrast, a higher relative abundance of Pseudomonas and Rhizobium, which are known to harbor many species with antagonistic properties to fungal pathogens, was found to be associated with susceptibility, indicating that these groups do not play a major role in genetically controlled resistance of oilseed rape against V. longisporum.

Download Full-text

Impact of Maize–Mushroom Intercropping on the Soil Bacterial Community Composition in Northeast China

Agronomy ◽

10.3390/agronomy10101526 ◽

2020 ◽

Vol 10 (10) ◽

pp. 1526

Author(s):

Xiaoqin Yang ◽

Yang Wang ◽

Luying Sun ◽

Xiaoning Qi ◽

Fengbin Song ◽

...

Keyword(s):

Bacterial Communities ◽

Northeast China ◽

Management Practice ◽

Bacterial Community Composition ◽

Soil Microbial Communities ◽

Chemical Properties ◽

Crop Productivity ◽

Rrna Gene ◽

Soil Bacterial Communities ◽

Soil Bacterial

Conservative agricultural practices have been adopted to improve soil quality and maintain crop productivity. An efficient intercropping of maize with mushroom has been developed in Northeast China. The objective of this study was to evaluate and compare the effects of planting patterns on the diversity and structure of the soil bacterial communities at a 0–20 cm depth in the black soil zone of Northeast China. The experiment consisted of monoculture of maize and mushroom, and intercropping in a split-plot arrangement. The characteristics of soil microbial communities were performed by 16S rRNA gene amplicom sequencing. The results showed that intercropping increased soil bacterial richness and diversity compared with maize monoculture. The relative abundances of Acidobacteria, Chloroflexi, Saccharibacteria and Planctomycetes were significantly higher, whereas Proteobacteria and Firmicutes were lower in intercropping than maize monoculture. Redundancy analysis suggested that pH, NO3−-N and NH4+-N contents had a notable effect on the structure of the bacterial communities. Moreover, intercropping significantly increased the relative abundance of carbohydrate metabolism pathway functional groups. Overall, these findings demonstrated that intercropping of maize with mushroom strongly impacts the physical and chemical properties of soil as well as the diversity and structure of the soil bacterial communities, suggesting this is a sustainable agricultural management practice in Northeast China.

Download Full-text

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.

Download Full-text

Diversity analysis and function prediction of rhizo- and endophytic bacterial communities of Senecio vulgaris L. (Asteraceae) in an invasive range

10.7287/peerj.preprints.26701v1 ◽

2018 ◽

Cited By ~ 1

Author(s):

Dandan Cheng ◽

Zhongsai Tian ◽

Liang Feng ◽

Lin Xu ◽

Hongmei Wang

Keyword(s):

Bacterial Communities ◽

Plant Pathogens ◽

Bacterial Community Composition ◽

Plant Invasions ◽

Function Prediction ◽

Alien Plants ◽

Central China ◽

Rrna Gene ◽

Mountainous Area ◽

Senecio Vulgaris

Because increasing evidence has confirmed the importance of plant-associated bacteria for plant growth and productivity, it is believed that interactions between bacteria and alien plants play an important role in plant invasions. However, the diversity of bacterial communities associated with invasive plants is poorly understood. Therefore, we investigated the diversity of rhizo- and endophytic bacteria associated with the invasive annual plant Senecio vulgaris L (Asteraceae) based on bacterial 16S rRNA gene data obtained from 57 samples of four S. vulgaris populations in a subtropical mountainous area in central China. Significant differences in diversity were observed between plant compartments. Rhizosphere harbored much more bacterial OTUs and showed higher alpha diversity than the leaf and root endosphere. Bacterial community composition differed substantially between compartments and locations in relative abundance profiles, especially at phyla and family level. However, the top five phyla (Proteobacteria, Firmicutes, Bacteroidetes, Actinobacteria and Acidobacteria) comprised more than 90% of abundance in all the bacterial communities. And similar endophytic communities with a shared core set of bacteria were observed from different S. vulgaris populations. According to the function prediction based on the identification and abundance information of the OTU, bacteria characterized as plant pathogens, as well as those involved in ureolysis and nitrate reduction, were rich in endophytic communities. This study reveals the microbiomes and their putative function in the invasive S. vulgaris plants and is also the first step for future studies on the role of interactions between bacteria and alien plants in plant invasions.

Download Full-text

The Presence of Denitrifiers In Bacterial Communities of Urban Stormwater Best Management Practices (BMPs)

Environmental Management ◽

10.1007/s00267-021-01529-z ◽

2021 ◽

Author(s):

Natalie C. Hall ◽

Masoumeh Sikaroodi ◽

Dianna Hogan ◽

R. Christian Jones ◽

Patrick M. Gillevet

Keyword(s):

Best Management Practices ◽

Bacterial Communities ◽

Management Practices ◽

Agricultural Land ◽

Bacterial Community Composition ◽

Rrna Gene ◽

Sand Filters ◽

Best Management ◽

Nitrogen Inputs ◽

Surface Sand

AbstractStormwater best management practices (BMPs) are engineered structures that attempt to mitigate the impacts of stormwater, which can include nitrogen inputs from the surrounding drainage area. The goal of this study was to assess bacterial community composition in different types of stormwater BMP soils to establish whether a particular BMP type harbors more denitrification potential. Soil sampling took place over the summer of 2015 following precipitation events. Soils were sampled from four bioretention facilities, four dry ponds, four surface sand filters, and one dry swale. 16S rRNA gene analysis of extracted DNA and RNA amplicons indicated high bacterial diversity in the soils of all BMP types sampled. An abundance of denitrifiers was also indicated in the extracted DNA using presence/absence of nirS, nirK, and nosZ denitrification genes. BMP soil bacterial communities were impacted by the surrounding soil physiochemistry. Based on the identification of a metabolically-active community of denitrifiers, this study has indicated that denitrification could potentially occur under appropriate conditions in all types of BMP sampled, including surface sand filters that are often viewed as providing low potential for denitrification. The carbon content of incoming stormwater could be providing bacterial communities with denitrification conditions. The findings of this study are especially relevant for land managers in watersheds with legacy nitrogen from former agricultural land use.

Download Full-text

Tree phyllosphere bacterial communities: exploring the magnitude of intra- and inter-individual variation among host species

PeerJ ◽

10.7717/peerj.2367 ◽

2016 ◽

Vol 4 ◽

pp. e2367 ◽

Cited By ~ 42

Author(s):

Isabelle Laforest-Lapointe ◽

Christian Messier ◽

Steven W. Kembel

Keyword(s):

Community Structure ◽

Bacterial Community ◽

Individual Variation ◽

Host Species ◽

Bacterial Communities ◽

Bacterial Community Structure ◽

Temperate Forest ◽

Abies Balsamea ◽

Tree Canopy ◽

Individual Tree

BackgroundThe diversity and composition of the microbial community of tree leaves (the phyllosphere) varies among trees and host species and along spatial, temporal, and environmental gradients. Phyllosphere community variation within the canopy of an individual tree exists but the importance of this variation relative to among-tree and among-species variation is poorly understood. Sampling techniques employed for phyllosphere studies include picking leaves from one canopy location to mixing randomly selected leaves from throughout the canopy. In this context, our goal was to characterize the relative importance of intra-individual variation in phyllosphere communities across multiple species, and compare this variation to inter-individual and interspecific variation of phyllosphere epiphytic bacterial communities in a natural temperate forest in Quebec, Canada.MethodsWe targeted five dominant temperate forest tree species including angiosperms and gymnosperms:Acer saccharum,Acer rubrum,Betula papyrifera,Abies balsameaandPicea glauca. For one randomly selected tree of each species, we sampled microbial communities at six distinct canopy locations: bottom-canopy (1–2 m height), the four cardinal points of mid-canopy (2–4 m height), and the top-canopy (4–6 m height). We also collected bottom-canopy leaves from five additional trees from each species.ResultsBased on an analysis of bacterial community structure measured via Illumina sequencing of the bacterial 16S gene, we demonstrate that 65% of the intra-individual variation in leaf bacterial community structure could be attributed to the effect of inter-individual and inter-specific differences while the effect of canopy location was not significant. In comparison, host species identity explains 47% of inter-individual and inter-specific variation in leaf bacterial community structure followed by individual identity (32%) and canopy location (6%).DiscussionOur results suggest that individual samples from consistent positions within the tree canopy from multiple individuals per species can be used to accurately quantify variation in phyllosphere bacterial community structure. However, the considerable amount of intra-individual variation within a tree canopy ask for a better understanding of how changes in leaf characteristics and local abiotic conditions drive spatial variation in the phyllosphere microbiome.

Download Full-text

Bacterial community characteristics and enzyme activities in Imperata cylindrica litter as phytoremediation progresses in a copper tailings dam

PeerJ ◽

10.7717/peerj.9612 ◽

2020 ◽

Vol 8 ◽

pp. e9612

Author(s):

Tong Jia ◽

Tingyan Guo ◽

Baofeng Chai

Keyword(s):

Bacterial Community ◽

Bacterial Communities ◽

Bacterial Community Composition ◽

Chemical Properties ◽

Alpha Diversity ◽

Imperata Cylindrica ◽

Copper Tailings ◽

Α Diversity ◽

Degraded Ecosystems ◽

And Function

This study analyzed Imperata cylindrica litter to determine variation in bacterial community composition and function along with enzyme activity as phytoremediation progresses. We found significant differences in physical and chemical properties of soil and litter in the different sub-dams investigated. The Actinobacteria, Gammaproteobacteria and Alphaproteobacteria were the dominant bacteria found in the litter of the different sub-dams. The alpha diversity (α-diversity) of litter bacterial community increased over as phytoremediation progressed, while total soil carbon and total litter carbon content were positively correlated to bacterial α-diversity. Total litter carbon and total nitrogen were the key factors that influenced bacterial community structure. Heavy metal can influence the degradation of litters by altering the composition of the microbial community. Furthermore, bacterial communities encoded with alpha-amylase (α-amylase) dominated during the initial phytoremediation stage; however, bacterial communities encoded with hemicellulase and peroxidase gradually dominated as phytoremediation progressed. Findings from this study provide a basis for exploring litter decomposition mechanisms in degraded ecosystems, which is critically important to understand the circulation of substances in copper tailings dams.

Download Full-text

Effects of Magnetic Minerals Exposure and Microbial Responses in Surface Sediment across the Bohai Sea

Microorganisms ◽

10.3390/microorganisms10010006 ◽

2021 ◽

Vol 10 (1) ◽

pp. 6

Author(s):

Lei Chen ◽

Mingpeng Wang ◽

Yuntao Li ◽

Weitao Shang ◽

Jianhui Tang ◽

...

Keyword(s):

Community Composition ◽

Surface Sediment ◽

Bohai Sea ◽

Bacterial Community Composition ◽

Microbial Community Composition ◽

Rrna Gene ◽

Sequencing Analysis ◽

Magnetic Minerals ◽

The Bohai Sea ◽

Α Diversity

Extensive production and application of magnetic minerals introduces significant amounts of magnetic wastes into the environment. Exposure to magnetic minerals could affect microbial community composition and geographic distribution. Here, we report that magnetic susceptibility is involved in determining bacterial α-diversity and community composition in surface sediment across the Bohai Sea by high-throughput sequencing analysis of the 16S rRNA gene. The results showed that environmental factors (explained 9.80%) played a larger role than spatial variables (explained 6.72%) in conditioning the bacterial community composition. Exposure to a magnetite center may shape the geographical distribution of five dissimilatory iron reducing bacteria. The microbial iron reduction ability and electroactive activity in sediment close to a magnetite center are stronger than those far away. Our study provides a novel understanding for the response of DIRB and electroactive bacteria to magnetic minerals exposure.

Download Full-text

Soil pH is the primary factor driving the distribution and function of microorganisms in farmland soils in northeastern China

Annals of Microbiology ◽

10.1007/s13213-019-01529-9 ◽

2019 ◽

Vol 69 (13) ◽

pp. 1461-1473 ◽

Cited By ~ 3

Author(s):

Cheng-yu Wang ◽

Xue Zhou ◽

Dan Guo ◽

Jiang-hua Zhao ◽

Li Yan ◽

...

Keyword(s):

Bacterial Community ◽

Soil Ph ◽

Bacterial Communities ◽

Nitrifying Bacteria ◽

Rrna Gene ◽

Ecological Functions ◽

Illumina Hiseq ◽

Α Diversity ◽

Farmland Soils ◽

Soil Bacterial

Abstract Purpose To understand which environmental factors influence the distribution and ecological functions of bacteria in agricultural soil. Method A broad range of farmland soils was sampled from 206 locations in Jilin province, China. We used 16S rRNA gene-based Illumina HiSeq sequencing to estimated soil bacterial community structure and functions. Result The dominant taxa in terms of abundance were found to be, Actinobacteria, Acidobacteria, Gemmatimonadetes, Chloroflexi, and Proteobacteria. Bacterial communities were dominantly affected by soil pH, whereas soil organic carbon did not have a significant influence on bacterial communities. Soil pH was significantly positively correlated with bacterial operational taxonomic unit abundance and soil bacterial α-diversity (P<0.05) spatially rather than with soil nutrients. Bacterial functions were estimated using FAPROTAX, and the relative abundance of anaerobic and aerobic chemoheterotrophs, and nitrifying bacteria was 27.66%, 26.14%, and 6.87%, respectively, of the total bacterial community. Generally, the results indicate that soil pH is more important than nutrients in shaping bacterial communities in agricultural soils, including their ecological functions and biogeographic distribution.

Download Full-text