scholarly journals Mineral Types and Tree Species Determine the Functional and Taxonomic Structures of Forest Soil Bacterial Communities

2016 ◽  
Vol 83 (5) ◽  
Author(s):  
Y. Colin ◽  
O. Nicolitch ◽  
M.-P. Turpault ◽  
S. Uroz
Keyword(s):  
Nutrient Cycling ◽  
Incubation Period ◽  
Tree Species ◽  
Bacterial Communities ◽  
Forest Ecosystems ◽  
Mineral Weathering ◽  
Content Type ◽  
Soil Bacterial Communities ◽  
Soil Bacterial ◽  
Mineral Type

ABSTRACT Although minerals represent important soil constituents, their impact on the diversity and structure of soil microbial communities remains poorly documented. In this study, pure mineral particles with various chemistries (i.e., obsidian, apatite, and calcite) were considered. Each mineral type was conditioned in mesh bags and incubated in soil below different tree stands (beech, coppice with standards, and Corsican pine) for 2.5 years to determine the relative impacts of mineralogy and mineral weatherability on the taxonomic and functional diversities of mineral-associated bacterial communities. After this incubation period, the minerals and the surrounding bulk soil were collected to determine mass loss and to perform soil analyses, enzymatic assays, and cultivation-dependent and -independent analyses. Notably, our 16S rRNA gene pyrosequencing analyses revealed that after the 2.5-year incubation period, the mineral-associated bacterial communities strongly differed from those of the surrounding bulk soil for all tree stands considered. When focusing only on minerals, our analyses showed that the bacterial communities associated with calcite, the less recalcitrant mineral type, significantly differed from those that colonized obsidian and apatite minerals. The cultivation-dependent analysis revealed significantly higher abundances of effective mineral-weathering bacteria on the most recalcitrant minerals (i.e., apatite and obsidian). Together, our data showed an enrichment of Betaproteobacteria and effective mineral-weathering bacteria related to the Burkholderia and Collimonas genera on the minerals, suggesting a key role for these taxa in mineral weathering and nutrient cycling in nutrient-poor forest ecosystems. IMPORTANCE Forests are usually developed on nutrient-poor and rocky soils, while nutrient-rich soils have been dedicated to agriculture. In this context, nutrient recycling and nutrient access are key processes in such environments. Deciphering how soil mineralogy influences the diversity, structure, and function of soil bacterial communities in relation to the soil conditions is crucial to better understanding the relative role of the soil bacterial communities in nutrient cycling and plant nutrition in nutrient-poor environments. The present study determined in detail the diversity and structure of bacterial communities associated with different mineral types incubated for 2.5 years in the soil under different tree species using cultivation-dependent and -independent analyses. Our data showed an enrichment of specific bacterial taxa on the minerals, specifically on the most weathered minerals, suggesting that they play key roles in mineral weathering and nutrient cycling in nutrient-poor forest ecosystems.

scholarly journals Pavement Overrides the Effects of Tree Species on Soil Bacterial Communities

2021 ◽  
Vol 18 (4) ◽  
pp. 2168
Author(s):  
Yinhong Hu ◽  
Weiwei Yu ◽  
Bowen Cui ◽  
Yuanyuan Chen ◽  
Hua Zheng ◽  
...  
Keyword(s):  
Bacterial Community ◽  
Bacterial Diversity ◽  
Community Composition ◽  
Tree Species ◽  
Bacterial Communities ◽  
Bacterial Community Composition ◽  
Soil Bacterial Community ◽  
Soil Bacterial Communities ◽  
Pine Stands ◽  
Soil Bacterial

Human disturbance and vegetation are known to affect soil microorganisms. However, the interacting effects of pavement and plant species on soil bacterial communities have received far less attention. In this study, we collected soil samples from pine (Pinus tabuliformis Carr.), ash (Fraxinus chinensis), and maple (Acer truncatum Bunge) stands that grew in impervious, pervious, and no pavement blocks to investigate the way pavement, tree species, and their interaction influence soil bacterial communities by modifying soil physicochemical properties. Soil bacterial community composition and diversity were evaluated by bacterial 16S amplicon sequencing. The results demonstrated that soil bacterial community composition and diversity did differ significantly across pavements, but not with tree species. The difference in soil bacterial community composition across pavements was greater in pine stands than ash and maple stands. Soil bacterial diversity and richness indices decreased beneath impervious pavement in pine stands, and only bacterial richness indices decreased markedly in ash stands, but neither showed a significant difference across pavements in maple stands. In addition, bacterial diversity did not differ dramatically between pervious pavement and no pavement soil. Taken together, these results suggest that pavement overwhelmed the effects of tree species on soil bacterial communities, and had a greater effect on soil bacterial communities in pine stands, followed by ash and maple stands. This study highlights the importance of anthropogenic disturbance, such as pavement, which affects soil microbial communities.

scholarly journals Responses of Bacterial Communities to Simulated Climate Changes in Alpine Meadow Soil of the Qinghai-Tibet Plateau

2015 ◽  
Vol 81 (17) ◽  
pp. 6070-6077 ◽  
Author(s):  
Junpeng Rui ◽  
Jiabao Li ◽  
Shiping Wang ◽  
Jiaxing An ◽  
Wen-tso Liu ◽  
...  
Keyword(s):  
Bacterial Community ◽  
Climate Warming ◽  
Bacterial Communities ◽  
Bacterial Community Structure ◽  
Climate Changes ◽  
Tibet Plateau ◽  
Content Type ◽  
Soil Bacterial Communities ◽  
Soil Bacterial ◽  
Qinghai Tibet Plateau

ABSTRACTThe soil microbial community plays an important role in terrestrial carbon and nitrogen cycling. However, microbial responses to climate warming or cooling remain poorly understood, limiting our ability to predict the consequences of future climate changes. To address this issue, it is critical to identify microbes sensitive to climate change and key driving factors shifting microbial communities. In this study, alpine soil transplant experiments were conducted downward or upward along an elevation gradient between 3,200 and 3,800 m in the Qinghai-Tibet plateau to simulate climate warming or cooling. After a 2-year soil transplant experiment, soil bacterial communities were analyzed by pyrosequencing of 16S rRNA gene amplicons. The results showed that the transplanted soil bacterial communities became more similar to those in their destination sites and more different from those in their “home” sites. Warming led to increases in the relative abundances inAlphaproteobacteria,Gammaproteobacteria, andActinobacteriaand decreases inAcidobacteria,Betaproteobacteria, andDeltaproteobacteria, while cooling had opposite effects on bacterial communities (symmetric response). Soil temperature and plant biomass contributed significantly to shaping the bacterial community structure. Overall, climate warming or cooling shifted the soil bacterial community structure mainly through species sorting, and such a shift might correlate to important biogeochemical processes such as greenhouse gas emissions. This study provides new insights into our understanding of soil bacterial community responses to climate warming and cooling.

scholarly journals A microcosm approach highlights the response of soil mineral weathering bacterial communities to an increase of K and Mg availability

2019 ◽  
Vol 9 (1) ◽  
Author(s):  
O. Nicolitch ◽  
M. Feucherolles ◽  
J.-L. Churin ◽  
L. Fauchery ◽  
M.-P. Turpault ◽  
...  
Keyword(s):  
Bacterial Communities ◽  
Forest Ecosystems ◽  
Base Cations ◽  
Mineral Weathering ◽  
Taxonomic Structure ◽  
Soil Mineral ◽  
Soil Bacterial Communities ◽  
Amplicon Pyrosequencing ◽  
Pcr Targeting

Abstract The access and recycling of the base cations are essential processes for the long-lasting functioning of forest ecosystems. While the role of soil bacterial communities has been demonstrated in mineral weathering and tree nutrition, our understanding of the link between the availability of base cations and the functioning of these communities remains limited. To fill this gap, we developed a microcosm approach to investigate how an increase in key base cations (potassium or magnesium) impacted the taxonomic and functional structures of the bacterial communities. During a 2-month period after fertilization with available potassium or magnesium, soil properties, global functions (metabolic potentials and respiration) as well as mineral weathering bioassays and 16S rRNA amplicon pyrosequencing were monitored. Our analyses showed no or small variations in the taxonomic structure, total densities and global functions between the treatments. In contrast, a decrease in the frequency and effectiveness of mineral weathering bacteria was observed in the fertilized treatments. Notably, quantitative PCR targeting specific genera known for their mineral weathering ability (i.e., Burkholderia and Collimonas) confirmed this decrease. These new results suggest that K and Mg cation availability drives the distribution of the mineral weathering bacterial communities in forest soil.

Response of soil bacterial communities to organic carbon input under soil freeze-thaw in forest ecosystems

2021 ◽  
Vol 105 ◽  
pp. 103333
Author(s):  
Hongmiao Yu ◽  
Limin Zhang ◽  
Yao Wang ◽  
Shengnan Xu ◽  
Yue Liu ◽  
...  
Keyword(s):  
Organic Carbon ◽  
Bacterial Communities ◽  
Forest Ecosystems ◽  
Freeze Thaw ◽  
Soil Bacterial Communities ◽  
Soil Bacterial

scholarly journals Global Biogeography and Quantitative Seasonal Dynamics of Gemmatimonadetes in Soil

2011 ◽  
Vol 77 (17) ◽  
pp. 6295-6300 ◽  
Author(s):  
Jennifer M. DeBruyn ◽  
Lauren T. Nixon ◽  
Mariam N. Fawaz ◽  
Amy M. Johnson ◽  
Mark Radosevich
Keyword(s):  
Soil Moisture ◽  
Seasonal Dynamics ◽  
Bacterial Communities ◽  
Present Evidence ◽  
Content Type ◽  
Soil Bacterial Communities ◽  
Soil Bacterial

ABSTRACTBacteria belonging to phylumGemmatimonadetescomprise approximately 2% of soil bacterial communities. However, little is known of their ecology due to a lack of cultured representation. Here we present evidence from biogeographical analyses and seasonal quantification ofGemmatimonadetesin soils, which suggests an adaptation to low soil moisture.

scholarly journals Identification of Soil Bacteria Susceptible to TiO2and ZnO Nanoparticles

2012 ◽  
Vol 78 (18) ◽  
pp. 6749-6758 ◽  
Author(s):  
Yuan Ge ◽  
Joshua P. Schimel ◽  
Patricia A. Holden
Keyword(s):  
Bacterial Communities ◽  
Soil Bacteria ◽  
Metal Oxide Nanoparticles ◽  
Engineered Nanoparticles ◽  
Dependent Manner ◽  
Soil Microcosms ◽  
Content Type ◽  
Soil Bacterial Communities ◽  
Soil Bacterial ◽  
Dose Dependent

ABSTRACTBecause soil is expected to be a major sink for engineered nanoparticles (ENPs) released to the environment, the effects of ENPs on soil processes and the organisms that carry them out should be understood. DNA-based fingerprinting analyses have shown that ENPs alter soil bacterial communities, but specific taxon changes remain unknown. We used bar-coded pyrosequencing to explore the responses of diverse bacterial taxa to two widely used ENPs, nano-TiO2and nano-ZnO, at various doses (0, 0.5, 1.0, and 2.0 mg g−1soil for TiO2; 0.05, 0.1, and 0.5 mg g−1soil for ZnO) in incubated soil microcosms. These ENPs significantly altered the bacterial communities in a dose-dependent manner, with some taxa increasing as a proportion of the community, but more taxa decreasing, indicating that effects mostly reduced diversity. Some of the declining taxa are known to be associated with nitrogen fixation (Rhizobiales,Bradyrhizobiaceae, andBradyrhizobium) and methane oxidation (Methylobacteriaceae), while some positively impacted taxa are known to be associated with the decomposition of recalcitrant organic pollutants (Sphingomonadaceae) and biopolymers including protein (StreptomycetaceaeandStreptomyces), indicating potential consequences to ecosystem-scale processes. The latter was suggested by a positive correlation between protease activity and the relative abundance ofStreptomycetaceae(R= 0.49,P= 0.000) andStreptomyces(R= 0.47,P= 0.000). Our results demonstrate that some metal oxide nanoparticles could affect soil bacterial communities and associated processes through effects on susceptible, narrow-function bacterial taxa.

Soil properties and tree species drive ß-diversity of soil bacterial communities

2014 ◽  
Vol 76 ◽  
pp. 201-209 ◽  
Author(s):  
William J. Landesman ◽  
David M. Nelson ◽  
Matthew C. Fitzpatrick
Keyword(s):  
Soil Properties ◽  
Tree Species ◽  
Bacterial Communities ◽  
Soil Bacterial Communities ◽  
Soil Bacterial
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