scholarly journals Groundwater Depth Overrides Tree-Species Effects on the Structure of Soil Microbial Communities Involved in Nitrogen Cycling in Plantation Forests

Forests ◽  
2020 ◽  
Vol 11 (3) ◽  
pp. 275 ◽  
Author(s):  
Tiehang Wu ◽  
Ashley Gray ◽  
Gan Liu ◽  
Hilary Kaminski ◽  
Bolanle Osi Efa ◽  
...  
Keyword(s):  
Microbial Communities ◽  
Nitrogen Cycling ◽  
Tree Species ◽  
Ammonia Oxidation ◽  
Soil Microbial Communities ◽  
Amoa Gene ◽  
Groundwater Depth ◽  
Functional Genes ◽  
Nitrification And Denitrification ◽  
Archaeal Communities

Microbial communities found in soil ecosystems play important roles in decomposing organic materials and recycling nutrients. A clear understanding on how biotic and abiotic factors influence the microbial community and its functional role in ecosystems is fundamental to terrestrial biogeochemistry and plant production. The purpose of this study was to investigate microbial communities and functional genes involved in nitrogen cycling as a function of groundwater depth (deep and shallow), tree species (pine and eucalypt), and season (spring and fall). Soil fungal, bacterial, and archaeal communities were determined by length heterogeneity polymerase chain reaction (LH-PCR). Soil ammonia oxidation archaeal (AOA) amoA gene, ammonia oxidation bacterial (AOB) amoA gene, nitrite oxidoreductase nrxA gene, and denitrifying bacterial narG, nirK, nirS, and nosZ genes were further studied using PCR and denaturing gradient gel electrophoresis (DGGE). Soil fungal and bacterial communities remained similar between tree species and groundwater depths, respectively, regardless of season. Soil archaeal communities remained similar between tree species but differed between groundwater depths in the spring only. Archaeal amoA for nitrification and bacterial nirK and nosZ genes for denitrification were detected in DGGE, whereas bacterial amoA and nrxA for nitrification and bacterial narG and nirS genes for denitrification were undetectable. The detected nitrification and denitrification communities varied significantly with groundwater depth. There was no significant difference of nitrifying archaeal amoA or denitrifying nirK communities between different tree species regardless of season. The seasonal difference in microbial communities and functional genes involved in nitrogen cycling suggests microorganisms exhibit seasonal dynamics that likely impact relative rates of nitrification and denitrification.

scholarly journals Linking microbial communities, functional genes and nitrogen-cycling processes in forest floors under four tree species

2016 ◽  
Vol 103 ◽  
pp. 181-191 ◽  
Author(s):  
Relena R. Ribbons ◽  
David J. Levy-Booth ◽  
Jacynthe Masse ◽  
Sue J. Grayston ◽  
Morag A. McDonald ◽  
...  
Keyword(s):  
Microbial Communities ◽  
Nitrogen Cycling ◽  
Tree Species ◽  
Functional Genes ◽  
Forest Floors

LDPE microplastics affect soil microbial communities and nitrogen cycling

2021 ◽  
Vol 773 ◽  
pp. 145640
Author(s):  
Lili Rong ◽  
Longfei Zhao ◽  
Leicheng Zhao ◽  
Zhipeng Cheng ◽  
Yiming Yao ◽  
...  
Keyword(s):  
Microbial Communities ◽  
Nitrogen Cycling ◽  
Soil Microbial Communities ◽  
Soil Microbial

scholarly journals Ecological and Genomic Attributes of Novel Bacterial Taxa That Thrive in Subsurface Soil Horizons

mBio ◽  
2019 ◽  
Vol 10 (5) ◽  
Author(s):  
Tess E. Brewer ◽  
Emma L. Aronson ◽  
Keshav Arogyaswamy ◽  
Sharon A. Billings ◽  
Jon K. Botthoff ◽  
...  
Keyword(s):  
United States ◽  
Microbial Communities ◽  
Soil Microbial Communities ◽  
The United States ◽  
Soil Profiles ◽  
Growth Strategies ◽  
Surface Soils ◽  
Wide Range ◽  
Bacterial And Archaeal Communities ◽  
Archaeal Communities

ABSTRACT While most bacterial and archaeal taxa living in surface soils remain undescribed, this problem is exacerbated in deeper soils, owing to the unique oligotrophic conditions found in the subsurface. Additionally, previous studies of soil microbiomes have focused almost exclusively on surface soils, even though the microbes living in deeper soils also play critical roles in a wide range of biogeochemical processes. We examined soils collected from 20 distinct profiles across the United States to characterize the bacterial and archaeal communities that live in subsurface soils and to determine whether there are consistent changes in soil microbial communities with depth across a wide range of soil and environmental conditions. We found that bacterial and archaeal diversity generally decreased with depth, as did the degree of similarity of microbial communities to those found in surface horizons. We observed five phyla that consistently increased in relative abundance with depth across our soil profiles: Chloroflexi, Nitrospirae, Euryarchaeota, and candidate phyla GAL15 and Dormibacteraeota (formerly AD3). Leveraging the unusually high abundance of Dormibacteraeota at depth, we assembled genomes representative of this candidate phylum and identified traits that are likely to be beneficial in low-nutrient environments, including the synthesis and storage of carbohydrates, the potential to use carbon monoxide (CO) as a supplemental energy source, and the ability to form spores. Together these attributes likely allow members of the candidate phylum Dormibacteraeota to flourish in deeper soils and provide insight into the survival and growth strategies employed by the microbes that thrive in oligotrophic soil environments. IMPORTANCE Soil profiles are rarely homogeneous. Resource availability and microbial abundances typically decrease with soil depth, but microbes found in deeper horizons are still important components of terrestrial ecosystems. By studying 20 soil profiles across the United States, we documented consistent changes in soil bacterial and archaeal communities with depth. Deeper soils harbored communities distinct from those of the more commonly studied surface horizons. Most notably, we found that the candidate phylum Dormibacteraeota (formerly AD3) was often dominant in subsurface soils, and we used genomes from uncultivated members of this group to identify why these taxa are able to thrive in such resource-limited environments. Simply digging deeper into soil can reveal a surprising number of novel microbes with unique adaptations to oligotrophic subsurface conditions.

scholarly journals Ecological and genomic attributes of novel bacterial taxa that thrive in subsurface soil horizons

2019 ◽  
Author(s):  
Tess E. Brewer ◽  
Emma L. Aronson ◽  
Keshav Arogyaswamy ◽  
Sharon A. Billings ◽  
Jon K. Botthoff ◽  
...  
Keyword(s):  
Microbial Communities ◽  
Soil Depth ◽  
Soil Microbial Communities ◽  
Soil Profiles ◽  
Growth Strategies ◽  
Surface Soils ◽  
Wide Range ◽  
Bacterial And Archaeal Communities ◽  
Archaeal Communities ◽  
The U.S

AbstractWhile most bacterial and archaeal taxa living in surface soils remain undescribed, this problem is exacerbated in deeper soils owing to the unique oligotrophic conditions found in the subsurface. Additionally, previous studies of soil microbiomes have focused almost exclusively on surface soils, even though the microbes living in deeper soils also play critical roles in a wide range of biogeochemical processes. We examined soils collected from 20 distinct profiles across the U.S. to characterize the bacterial and archaeal communities that live in subsurface soils and to determine whether there are consistent changes in soil microbial communities with depth across a wide range of soil and environmental conditions. We found that bacterial and archaeal diversity generally decreased with depth, as did the degree of similarity of microbial communities to those found in surface horizons. We observed five phyla that consistently increased in relative abundance with depth across our soil profiles: Chloroflexi, Nitrospirae, Euryarchaeota, and candidate phyla GAL15 and Dormibacteraeota (formerly AD3). Leveraging the unusually high abundance of Dormibacteraeota at depth, we assembled genomes representative of this candidate phylum and identified traits that are likely to be beneficial in low nutrient environments, including the synthesis and storage of carbohydrates, the potential to use carbon monoxide (CO) as a supplemental energy source, and the ability to form spores. Together these attributes likely allow members of the candidate phylum Dormibacteraeota to flourish in deeper soils and provide insight into the survival and growth strategies employed by the microbes that thrive in oligotrophic soil environments.ImportanceSoil profiles are rarely homogeneous. Resource availability and microbial abundances typically decrease with soil depth, but microbes found in deeper horizons are still important components of terrestrial ecosystems. By studying 20 soil profiles across the U.S., we documented consistent changes in soil bacterial and archaeal communities with depth. Deeper soils harbored distinct communities compared to the more commonly studied surface horizons. Most notably, we found that the candidate phylum Dormibacteraeota (formerly AD3) was often dominant in subsurface soils, and we used genomes from uncultivated members of this group to identify why these taxa are able to thrive in such resource-limited environments. Simply digging deeper into soil can reveal a surprising amount of novel microbes with unique adaptations to oligotrophic subsurface conditions.

Soil and tree species traits both shape soil microbial communities during early growth of Chinese subtropical forests

2016 ◽  
Vol 96 ◽  
pp. 180-190 ◽  
Author(s):  
Zhiqin Pei ◽  
David Eichenberg ◽  
Helge Bruelheide ◽  
Wenzel Kröber ◽  
Peter Kühn ◽  
...  
Keyword(s):  
Microbial Communities ◽  
Tree Species ◽  
Soil Microbial Communities ◽  
Species Traits ◽  
Early Growth ◽  
Subtropical Forests ◽  
Soil Microbial

scholarly journals Functional Gene Differences in Soil Microbial Communities from Conventional, Low-Input, and Organic Farmlands

2012 ◽  
Vol 79 (4) ◽  
pp. 1284-1292 ◽  
Author(s):  
Kai Xue ◽  
Liyou Wu ◽  
Ye Deng ◽  
Zhili He ◽  
Joy Van Nostrand ◽  
...  
Keyword(s):  
Microbial Communities ◽  
Agricultural Research ◽  
Microbial Community Composition ◽  
Soil Microbial Communities ◽  
Functional Gene ◽  
Functional Genes ◽  
N Availability ◽  
Low Input ◽  
Soil Microbial ◽  
Denitrification Genes

ABSTRACTVarious agriculture management practices may have distinct influences on soil microbial communities and their ecological functions. In this study, we utilized GeoChip, a high-throughput microarray-based technique containing approximately 28,000 probes for genes involved in nitrogen (N)/carbon (C)/sulfur (S)/phosphorus (P) cycles and other processes, to evaluate the potential functions of soil microbial communities under conventional (CT), low-input (LI), and organic (ORG) management systems at an agricultural research site in Michigan. Compared to CT, a high diversity of functional genes was observed in LI. The functional gene diversity in ORG did not differ significantly from that of either CT or LI. Abundances of genes encoding enzymes involved in C/N/P/S cycles were generally lower in CT than in LI or ORG, with the exceptions of genes in pathways for lignin degradation, methane generation/oxidation, and assimilatory N reduction, which all remained unchanged. Canonical correlation analysis showed that selected soil (bulk density, pH, cation exchange capacity, total C, C/N ratio, NO3−, NH4+, available phosphorus content, and available potassium content) and crop (seed and whole biomass) variables could explain 69.5% of the variation of soil microbial community composition. Also, significant correlations were observed between NO3−concentration and denitrification genes, NH4+concentration and ammonification genes, and N2O flux and denitrification genes, indicating a close linkage between soil N availability or process and associated functional genes.

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