scholarly journals Long-Term N Fertilization Decreased Diversity and Altered the Composition of Soil Bacterial and Archaeal Communities

Agronomy ◽  
2019 ◽  
Vol 9 (10) ◽  
pp. 574 ◽  
Author(s):  
Renpeng Sun ◽  
Pan Zhang ◽  
Chance W. Riggins ◽  
María C. Zabaloy ◽  
Sandra Rodríguez-Zas ◽  
...  
Keyword(s):  
Crop Production ◽  
Soil Microbial Communities ◽  
N Fertilization ◽  
Rrna Gene ◽  
Maize Production ◽  
Soil Microbial ◽  
Continuous Maize ◽  
Bacterial And Archaeal Communities ◽  
Soil Bacterial ◽  
Archaeal Communities

Soil microbial communities are essential in the cycling of nutrients that affect crop production. Our goal was to characterize the microbial community structure following 34 years of nitrogen (N) fertilization treatments in continuous maize production in highly fertile soils. Using 16S rRNA gene-based analysis of the V4 region via Illumina HiSeq2500 technology with downstream bioinformatics processing and analysis with QIIME 2.0, we aimed to characterize the prokaryotic communities under three increasing N fertilization rates. Factor analyses indicated that a high N level decreased the diversity of soil bacterial and archaeal communities and altered the relative abundance (RA) of the dominant (>1% RA) and minor (<1% RA) phyla. Among the 12 major phyla, we determined increases in Gemmatimonadetes, Proteobacteria, and Euryarchaeota, accompanied by reductions in Cyanobacteria, Chloroflexi, Firmicutes, and Planctomycetes with increasing N. Within the 29 minor phyla, N fertilization led to increases in Aquificae, WPS2, Parvarchaeota, AD3, FCPU426, Armatimonadetes, TM7, Chlamydiae, and OD1, along with reductions of Nitrospirae, WS3, Tenericutes, Lentisphaerae, OP3, Synergistetes, Thermotogae, and prokaryotes that could not be reliably assigned to a phylum (classified as Other).

scholarly journals Phylogenetic Clustering of Soil Microbial Communities by 16S rRNA but Not 16S rRNA Genes

2012 ◽  
Vol 78 (7) ◽  
pp. 2459-2461 ◽  
Author(s):  
Kristen M. DeAngelis ◽  
Mary K. Firestone
Keyword(s):  
16S Rrna ◽  
Soil Microbial Communities ◽  
16S Rrna Genes ◽  
Rrna Genes ◽  
Rrna Gene ◽  
Phylogenetic Clustering ◽  
Soil Microbial ◽  
Highly Active ◽  
Bacterial And Archaeal Communities ◽  
Archaeal Communities

ABSTRACTWe evaluated phylogenetic clustering of bacterial and archaeal communities from redox-dynamic subtropical forest soils that were defined by 16S rRNA and rRNA gene sequences. We observed significant clustering for the RNA-based communities but not the DNA-based communities, as well as increasing clustering over time of the highly active taxa detected by only rRNA.

scholarly journals Alteration of Nutrient Substrates and Absence of Seawater Due to Coastal Embankments Affects Soil Microbial Communities in Salt Marshes of Eastern China

2021 ◽  
Author(s):  
Hongyu Feng ◽  
Yajun Qiao ◽  
Lu Xia ◽  
Wen Yang ◽  
Yongqiang Zhao ◽  
...  
Keyword(s):  
Physicochemical Properties ◽  
Eastern China ◽  
Soil Microbial Communities ◽  
Soil Nutrient ◽  
Rrna Gene ◽  
Soil Physicochemical Properties ◽  
Organic C ◽  
Soil Microbial ◽  
Bacterial And Archaeal Communities ◽  
Archaeal Communities

Abstract Aims: Although the influence of coastal embankments on soil physicochemical properties and carbon (C) and nitrogen (N) cycling has been widely studied, the mechanisms of their effects on the soil microbial ecology are still poorly understood. Thus, the aim of this study was to investigate variations in soil bacterial and archaeal communities between natural and embanked saltmarshes, as well as the determinants that drive these variations.Methods: 16S rRNA gene sequence analysis was performed to assess the impacts of embankments on the bacterial and archaeal communities of the invasive Spartina alterniflora Loisel., as well as native Suaeda salsa (L.) Pall. and Phragmites australis (Cav.) Trin. ex Steud. saltmarshes in the coastal China.Results: Embankments significantly decreased the Simpson diversity index of the S. alterniflora saltmarsh, while increasing the OTU richness in the P. australis saltmarsh. Additionally, the bacterial and archaeal community compositions in the embanked S. alterniflora and P. australis saltmarshes were considerably modified. However, no variations were found between the bacterial and archaeal communities of the natural and embanked S. salsa saltmarshes.Conclusions: These results were possibly because embankments decreased the soil nutrient substrates (e.g., soil organic C and N) dramatically in the S. alterniflora saltmarsh, while increased soil nutrient substrates significantly in the P. australis saltmarsh. However, embankments had a negligible effect on the soil nutrient substrates in the S. salsa saltmarsh. Moreover, embankments increased the abundance of Betaproteobacteria, and decreased the abundance of sulfur- and sodium-dependent bacteria due to the dramatic change in soil physicochemical properties.

scholarly journals Urbanization-induced environmental changes strongly affect wetland soil bacterial community composition and diversity

2021 ◽  
Author(s):  
Xinyu Yi ◽  
Chen Ning ◽  
Shuailong Feng ◽  
Haiqiang Gao ◽  
Jianlun Zhao ◽  
...  
Keyword(s):  
Bacterial Community ◽  
Bacterial Communities ◽  
Environmental Changes ◽  
Bacterial Community Composition ◽  
Soil Microbial Communities ◽  
Environmental Drivers ◽  
Wetland Soil ◽  
Rrna Gene ◽  
Soil Microbial ◽  
Soil Bacterial

Abstract Soil microbial communities potentially serve as indicators for their responses to changes in various ecosystems at scales from a region to the globe. However, changes in wetland soil bacterial communities and how they are related to urbanization intensities remains poorly understood. Here, we collected sixty soil samples along urbanization intensity gradients from twenty wetlands. We measured a range of environmental factors and characterized bacterial communities structure using 16S rRNA gene amplicon sequencing that targeted the V4-V5 region. Our results revealed the dominant soil microbial phyla included Proteobacteria (39.3%), Acidobacteria (21.4%) and Chloroflexi (12.3%) in the wetlands, and showed a significant divergence of composition in intensive urbanization area (UI_4) than other places. A critical "threshold" exists in the soil bacterial diversity, demonstrating different patterns: a gradual increase in the areas of low-to-intermediate disturbances but a significant decrease in highly urbanized areas where metabolic functions were significantly strong. Additionally, soil pH, total phosphorus (TP), available phosphorus (AP ) and ammonia nitrogen (NH4+-N) made a significant contribution to variations in bacterial communities, explaining 49.6%, 35.1%, 26.2% and 30.7% of the total variance, respectively. pH and NH4+-N were identified as the main environmental drivers to determine bacterial community structure and diversity in the urban wetlands. Our results highlight collective changes in multiple environmental variables induced by urbanization rather than by the proportion of impervious surface area (ISA), which were potentially attributed to the spatial heterogeneity along different urbanization gradients.

scholarly journals Long-Term Drought and Warming Alter Soil Bacterial and Fungal Communities in an Upland Heathland

Ecosystems ◽  
2021 ◽  
Author(s):  
Fiona M. Seaton ◽  
Sabine Reinsch ◽  
Tim Goodall ◽  
Nicola White ◽  
Davey L. Jones ◽  
...  
Keyword(s):  
Climate Change ◽  
Microbial Communities ◽  
Soil Microbial Communities ◽  
Fungal Communities ◽  
Its2 Region ◽  
Rrna Gene ◽  
Summer Drought ◽  
Soil Microbial ◽  
Soil Bacterial

AbstractThe response of soil microbial communities to a changing climate will impact global biogeochemical cycles, potentially leading to positive and negative feedbacks. However, our understanding of how soil microbial communities respond to climate change and the implications of these changes for future soil function is limited. Here, we assess the response of soil bacterial and fungal communities to long-term experimental climate change in a heathland organo-mineral soil. We analysed microbial communities using Illumina sequencing of the 16S rRNA gene and ITS2 region at two depths, from plots undergoing 4 and 18 years of in situ summer drought or warming. We also assessed the colonisation of Calluna vulgaris roots by ericoid and dark septate endophytic (DSE) fungi using microscopy after 16 years of climate treatment. We found significant changes in both the bacterial and fungal communities in response to drought and warming, likely mediated by changes in soil pH and electrical conductivity. Changes in the microbial communities were more pronounced after a longer period of climate manipulation. Additionally, the subsoil communities of the long-term warmed plots became similar to the topsoil. Ericoid mycorrhizal colonisation decreased with depth while DSEs increased; however, these trends with depth were removed by warming. We largely ascribe the observed changes in microbial communities to shifts in plant cover and subsequent feedback on soil physicochemical properties, especially pH. Our results demonstrate the importance of considering changes in soil microbial responses to climate change across different soil depths and after extended periods of time.

scholarly journals Microbial communities and soil chemical features associated with commercial production of the medicinal mushroom Ganoderma lingzhi in soil

2019 ◽  
Vol 9 (1) ◽  
Author(s):  
Le-Qin Ke ◽  
Pu-Dong Li ◽  
Jian-Ping Xu ◽  
Qiu-Shuang Wang ◽  
Liang-Liang Wang ◽  
...  
Keyword(s):  
Microbial Communities ◽  
Crop Production ◽  
Soil Microbial Communities ◽  
Rrna Gene ◽  
Medicinal Mushroom ◽  
Nitrogen And Phosphorus ◽  
Illumina Hiseq ◽  
Soil Microbial ◽  
Dead Trees ◽  
Ganoderma Lingzhi

Abstract Crop production, including mushroom farming, may cause significant changes to the underlying substrates which in turn, can influence crop quality and quantity during subsequent years. Here in this study, we analyzed the production of the medicinal mushroom Ganoderma lingzhi and the associated soil microbial communities and soil chemical features over 24 months from April 2015 to April 2017. This Basidiomycete mushroom, known as Lingzhi in China, is commonly found on dead trees and wood logs in temperate and subtropical forests. Its economic and medicinal importance have propelled the development of a diversity of cultivation methods. The dominant method uses wood logs as the main substrate, which after colonization by Lingzhi mycelia, are buried in the soil to induce fruiting. The soil microbial communities over the 24 months were analyzed using the Illumina HiSeq platform targeting a portion of the bacterial 16S rRNA gene and the fungal internal transcribed spacer 1 (ITS1). Overall, a significant reduction of Lingzhi yield was observed over our experimentation period. Interestingly, temporal changes in soil microbial compositions were detected during the 24 months, with the fungal community showing more changes than that of bacteria in terms of both species richness and the relative abundance of several dominant species after each fruiting. The soil chemical features also showed significant changes, with decreasing soil nitrogen and phosphorus concentrations and increasing soil pH and iron content after each fruiting. We discuss the implications of our results in sustainable Lingzhi production in soil.

scholarly journals Plant Growth Modifications Due to Coastal Embankments Affect Soil Bacterial and Archaeal Communities Over the Growing Season in Salt Marshes of Eastern China

2022 ◽  
Author(s):  
Hongyu Feng ◽  
Yajun Qiao ◽  
Lu Xia ◽  
Wen Yang ◽  
Yongqiang Zhao ◽  
...  
Keyword(s):  
Salt Marsh ◽  
Microbial Diversity ◽  
Soil Properties ◽  
Salt Marshes ◽  
Soil Nutrient ◽  
Rrna Gene ◽  
Organic C ◽  
Bacterial And Archaeal Communities ◽  
Soil Bacterial ◽  
Archaeal Communities

Abstract Aims: Although the influences of coastal embankments on physicochemical soil properties and carbon (C) and nitrogen (N) cycling have been widely studied, the mechanisms of their effects on soil microbial ecologies remain poorly understood. Thus, the aim of this study was to investigate variations in the diversity and composition of soil bacterial and archaeal communities between natural and embanked saltmarshes, as well as the determinants that drive these variations.Methods: 16S rRNA gene sequence analysis was performed to assess the impacts of embankments on the bacterial and archaeal communities of native Suaeda salsa, Phragmites australis, and invasive Spartina alterniflora saltmarshes on the east coast of China.Results: Embankments were found to significantly decrease the microbial diversity of the S. alterniflora salt marsh, while they increased the OTU richness of the P. australis salt marsh. Embankments modified the compositions of soil bacterial and archaeal communities in both the S. alterniflora and P. australis salt marshes. However, variations in the microbial diversity, richness, and community compositions between the native and embanked S. salsa salt marshes were insignificant. Conclusions: These results were possibly because the embankment significantly altered soil nutrient substrate levels (e.g., soil organic C and N) by variations in plant residues and physiochemical soil properties in S. alterniflora and P. australis saltmarshes, whereas the embankment had no observable changes in the soil nutrient substrate and the plant residue in S. salsa saltmarsh. This study also elucidated the effects of coastal embankments on biogeochemical cycles, and highlighted their potential hazards to ecosystems.

scholarly journals Effects of biodegradable plastic film mulching on soil microbial communities in two agroecosystems

PeerJ ◽  
2020 ◽  
Vol 8 ◽  
pp. e9015 ◽  
Author(s):  
Sreejata Bandopadhyay ◽  
Henry Y. Sintim ◽  
Jennifer M. DeBruyn
Keyword(s):  
Community Structure ◽  
Microbial Communities ◽  
Crop Production ◽  
Soil Microbial Communities ◽  
Biodegradable Plastic ◽  
Rrna Gene ◽  
Plastic Mulch ◽  
Soil Microbial Community Structure ◽  
Soil Microbial ◽  
Mulch Films

Plastic mulch films are used globally in crop production but incur considerable disposal and environmental pollution issues. Biodegradable plastic mulch films (BDMs), an alternative to polyethylene (PE)-based films, are designed to be tilled into the soil where they are expected to be mineralized to carbon dioxide, water and microbial biomass. However, insufficient research regarding the impacts of repeated soil incorporation of BDMs on soil microbial communities has partly contributed to limited adoption of BDMs. In this study, we evaluated the effects of BDM incorporation on soil microbial community structure and function over two years in two geographical locations: Knoxville, TN, and in Mount Vernon, WA, USA. Treatments included four plastic BDMs (three commercially available and one experimental film), a biodegradable cellulose paper mulch, a non-biodegradable PE mulch and a no mulch plot. Bacterial community structure determined using 16S rRNA gene amplicon sequencing revealed significant differences by location and season. Differences in bacterial communities by mulch treatment were not significant for any season in either location, except for Fall 2015 in WA where differences were observed between BDMs and no-mulch plots. Extracellular enzyme assays were used to characterize communities functionally, revealing significant differences by location and sampling season in both TN and WA but minimal differences between BDMs and PE treatments. Overall, BDMs had comparable influences on soil microbial communities to PE mulch films.

scholarly journals Associations between human impacts and forest soil microbial communities

Elem Sci Anth ◽  
2020 ◽  
Vol 8 (1) ◽  
Author(s):  
Yongjian Chen ◽  
Jialiang Kuang ◽  
Pandeng Wang ◽  
Wensheng Shu ◽  
Albert Barberán
Keyword(s):  
Microbial Communities ◽  
Forest Soil ◽  
Human Activity ◽  
Eastern China ◽  
Soil Microbial Communities ◽  
Nitrifying Bacteria ◽  
Rrna Gene ◽  
Internal Transcribed Spacer Region ◽  
Soil Microbial ◽  
Soil Variables

We are living in a new epoch—the Anthropocene, in which human activity is reshaping global biodiversity at an unprecedented rate. Increasing efforts are being made toward a better understanding of the associations between human activity and the geographic patterns in plant and animal communities. However, similar efforts are rarely applied to microbial communities. Here, we collected 472 forest soil samples across eastern China, and the bacterial and fungal communities in those samples were determined by high-throughput sequencing of 16S rRNA gene and internal transcribed spacer region, respectively. By compiling human impact variables as well as climate and soil variables, our goal was to elucidate the association between microbial richness and human activity when climate and soil variables are taken into account. We found that soil microbial richness was associated with human activity. Specifically, human population density was positively associated with the richness of bacteria, nitrifying bacteria and fungal plant pathogens, but it was negatively associated with the richness of cellulolytic bacteria and ectomycorrhizal fungi. Together, these results suggest that the associations between geographic variations of soil microbial richness and human activity still persist when climate and soil variables are taken into account and that these associations vary among different microbial taxonomic and functional groups.

Soil bacterial communities interact with silicon fraction transformation and promote rice yield after long-term straw return

2021 ◽  
Author(s):  
Alin Song ◽  
Zimin Li ◽  
Fenliang Fan
Keyword(s):  
Microbial Community ◽  
Rice Yield ◽  
Soil Microbial Communities ◽  
Nutrient Sources ◽  
Soil Microbial ◽  
Mn Oxide ◽  
Straw Return ◽  
Soil Bacterial ◽  
Healthy Growth

&lt;p&gt;Returning crop straw into soil is an important practice to balance biogenic and bioavailable silicon (Si) pool in paddy, which is crucial for rice healthy growth. However, it remains elusive how straw return affects Si bioavailability, its uptake, and rice yield, owing to little knowledge about soil microbial communities responsible for straw degradation. Here, we investigated the change of soil Si fractions and microbial community in a 39-year-old paddy field amended by a long-term straw return. Results showed that rice straw-return significantly increased soil bioavailable Si and rice yield to from 29.9% to 61.6% and from 14.5% to 23.6%, respectively, compared to NPK fertilization alone. Straw return significantly altered soil microbial community abundance. Acidobacteria was positively and significantly related to amorphous Si, while Rokubacteria at the phylum level, Deltaproteobacteria and Holophagae at the class level were negatively and significantly related to organic matter adsorbed and Fe/Mn-oxide combined Si in soils. Redundancy analysis of their correlations further demonstrated that Si status significantly explained 12% of soil bacterial community variation. These findings suggest that soil bacteria community and diversity interact with Si mobility via altering its transformation, resulting in the balance of various nutrient sources to drive biological silicon cycle in agroecosystem.&lt;/p&gt;

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