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 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 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 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 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.

scholarly journals Manure substitution of chemical fertilizer affect soil microbial community diversity, structure and function in greenhouse vegetable production systems

2019 ◽  
Author(s):  
Haoan Luan ◽  
Wei Gao ◽  
Shaowen Huang ◽  
Jiwei Tang ◽  
Mingyue Li ◽  
...  
Keyword(s):  
Microbial Community ◽  
Physicochemical Properties ◽  
Soil Microbial Community ◽  
Enzyme Activities ◽  
Substitution Rate ◽  
Soil Microbial Communities ◽  
Chemical Fertilizer ◽  
Soil Physicochemical Properties ◽  
Soil Microbial ◽  
Microbial Characteristics

ABSTRACTSoil microbial community and enzyme activities together affect various ecosystem functions of soils. Fertilization, as important agricultural management practices, are known to modify soil microbial characteristics; however, inconsistent results have been reported. The aim of this research therefore was to make a comparative study of the effects of different fertilization patterns (No N inputs (No N), 100% chemical fertilizer-N (CN) inputs (4/4CN) and different substitution rates of CN by organic manure-N (MN) (3/4CN+1/4MN, 2/4CN+2/4MN and 1/4CN+3/4MN)) on soil physicochemical properties, enzyme activities and microbial attributes in a GVP of Tianjin, China. Manure substitution of chemical fertilizer, especially at higher substitution rate (2/4CN+2/4MN and 1/4CN+3/4MN), improved soil physicochemical properties (higher soil organic C (SOC) and nutrient contents; lower bulk densities), promoted microbial growth (higher total phospholipid fatty acids and microbial biomass C contents) and activity (higher soil hydrolase activities). Manure addition caused a remarkable increase of the fungi/bacteria ratio and a distinct shift in the fungal (bacterial) community to greater abundance of arbuscular mycorrhizal fungi (G+ bacteria) compared with saprotrophic fungi (G− bacteria). These changes drove shifts toward fungal-dominated soil microbial communities and then optimized microbial community structure. Also, manure application increased soil biodiversity (microbial community and enzyme function), indicated by increased Shannon–Wiener diversity. Redundancy analysis indicated that the most possible mechanism of the impacts of different fertilization patterns on soil microbial characteristics may be the mediation of SOC and nutrient (N) availability (especially SOC) in this GVP of China. In conclusion, manure substitution of chemical fertilizer, especially at higher substitution rate, was more efficient for improving soil quality and biological functions.

scholarly journals Petroleum-contamination drives the shift of microbiome through modifying soil metallome

2021 ◽  
Author(s):  
Zhe Liu ◽  
Meixia Gu ◽  
Wei Zhu ◽  
Mengru Zhang ◽  
Weizhi Zhou
Keyword(s):  
Physicochemical Properties ◽  
Soil Microbial Communities ◽  
Oil Field ◽  
Total Carbon ◽  
Petroleum Contamination ◽  
Soil Physicochemical Properties ◽  
Short Term ◽  
Soil Microbial ◽  
Microbial Network ◽  
Α Diversity

Soil oil-pollution is one of the most severe environmental issues at present. Shifts of soil metallome and microbiome are essential indicators for risk assessment and remediation of field soil pollutions, but not well studied undergoing the petroleum contamination. In this research, soil samples were collected from a short-term and long-term petroleum-contaminated oil field. The soil physicochemical properties, metallome, microbial community, and polluted and unpolluted soil network were testified. Results showed that the contents of soil total petroleum hydrocarbon, total carbon, total nitrogen, total sulfur, total phosphorus, calcium, copper, manganese, lead, and zinc were increased by petroleum contamination. In contrast, the soil pH was decreased by petroleum contamination regardless of the pollution duration. Petroleum-contamination also reduced bacterial and fungal α-diversity indices. In contrast, bacterial α-diversity was negatively correlated with soil TPH and EC, and fungal α-diversity was negatively correlated with soil EC. Moreover, the relative abundances of Proteobacteria, Ascomycota, Oleibacter, and Fusarium in soil were increased by petroleum contamination. Network analysis showed that number of links, modules and the network invulnerability decreased in PS, followed by the OS group. These results demonstrate that short-term heavy petroleum contamination can cause shifts in soil physicochemical properties, metallome, and microbiome and assemble a less complex and vulnerable soil microbial network. Moreover, natural restoration can hardly amend soil properties and microbial network structure. This research emphasizes that the uncommonly studied soil metallome may play a vital part in the reaction of soil microbial communities to petroleum-contamination and potential application value of synthetic community in bioremediation.

scholarly journals Coupling Effects of Goat Manure and Water Management on Immobilization of Cadmium and Improvement of Bacterial Community

2022 ◽  
Author(s):  
Yiyun Liu ◽  
Yingming Xu ◽  
Qingqing Huang ◽  
Xu Qin ◽  
Lijie Zhao ◽  
...  
Keyword(s):  
Water Management ◽  
Bacterial Community ◽  
Physicochemical Properties ◽  
Soil Microbial Communities ◽  
Soil Physicochemical Properties ◽  
Water Condition ◽  
Soil Microbial ◽  
Goat Manure ◽  
Remediation Process ◽  
Amended Soil

Abstract The objective of this study was to expound possible effect of fertilization and water management in the remediation process of hazardous substance using sepiolite(SP). Meanwhile, Illumina high-throughput sequencing was performed to investigate how the composition of the rhizosphere bacterial community responded to a series of soil remediation process. The results showed that application of SP increased pH, decreased DOM under different water condition, but goat manure (GM) increased pH and DOM at the same time. Under water-saturated condition (FWHC), the application of GM increased the content of available Cd (DTPA-Cd) by 42.0-68.9%, 13.1%-30.3% of unamended and SP-amended soil, respectively. Under normal water condition (NWHC), the application of GM increased DTPA-Cd by 0.7%-5.8%, 73.7%-115.5% of unamended and SP-amended soil, respectively. Consequently, coupling effect of FWHC and GM decreased Cd content in shoots of pak choi. We also found that the application of GM increased the abundance of soil microbial communities. Abundance of proteobacteria reached a peak when applied GM in SP-amended soil under FWHC. RDA analysis showed that soil microbes such as bacteroidetes, patescibacteria, and proteobacteria were correlated positively with pH, DOM, and DTPA-Cd. Acidobacteria was correlated positively with DTPA-Cd, and negatively with pH and DOM. The relationship of soil physicochemical properties and the bacterial community variation indicated that GM and SP mixed additives may indirectly affect the soil microbial community by changing soil physicochemical properties and available Cd content.

scholarly journals Distinct Biogeographic Patterns for Archaea, Bacteria, and Fungi along the Vegetation Gradient at the Continental Scale in Eastern China

mSystems ◽  
2017 ◽  
Vol 2 (1) ◽  
Author(s):  
Bin Ma ◽  
Zhongmin Dai ◽  
Haizhen Wang ◽  
Melissa Dsouza ◽  
Xingmei Liu ◽  
...  
Keyword(s):  
Eastern China ◽  
Soil Microbial Communities ◽  
Natural Forest ◽  
Community Diversity ◽  
Biogeographic Patterns ◽  
Soil Microbial ◽  
Continental Scale ◽  
Forest Sites ◽  
Vegetation Gradient ◽  
Bacteria And Fungi

ABSTRACT Understanding biogeographic patterns is a precursor to improving our knowledge of the function of microbiomes and to predicting ecosystem responses to environmental change. Using natural forest soil samples from 110 locations, this study is one of the largest attempts to comprehensively understand the different patterns of soil archaeal, bacterial, and fungal biogeography at the continental scale in eastern China. These patterns in natural forest sites could ascertain reliable soil microbial biogeographic patterns by eliminating anthropogenic influences. This information provides guidelines for monitoring the belowground ecosystem’s decline and restoration. Meanwhile, the deviations in the soil microbial communities from corresponding natural forest states indicate the extent of degradation of the soil ecosystem. Moreover, given the association between vegetation type and the microbial community, this information could be used to predict the long-term response of the underground ecosystem to the vegetation distribution caused by global climate change. The natural forest ecosystem in Eastern China, from tropical forest to boreal forest, has declined due to cropland development during the last 300 years, yet little is known about the historical biogeographic patterns and driving processes for the major domains of microorganisms along this continental-scale natural vegetation gradient. We predicted the biogeographic patterns of soil archaeal, bacterial, and fungal communities across 110 natural forest sites along a transect across four vegetation zones in Eastern China. The distance decay relationships demonstrated the distinct biogeographic patterns of archaeal, bacterial, and fungal communities. While historical processes mainly influenced bacterial community variations, spatially autocorrelated environmental variables mainly influenced the fungal community. Archaea did not display a distance decay pattern along the vegetation gradient. Bacterial community diversity and structure were correlated with the ratio of acid oxalate-soluble Fe to free Fe oxides (Feo/Fed ratio). Fungal community diversity and structure were influenced by dissolved organic carbon (DOC) and free aluminum (Ald), respectively. The role of these environmental variables was confirmed by the correlations between dominant operational taxonomic units (OTUs) and edaphic variables. However, most of the dominant OTUs were not correlated with the major driving variables for the entire communities. These results demonstrate that soil archaea, bacteria, and fungi have different biogeographic patterns and driving processes along this continental-scale natural vegetation gradient, implying different community assembly mechanisms and ecological functions for archaea, bacteria, and fungi in soil ecosystems. IMPORTANCE Understanding biogeographic patterns is a precursor to improving our knowledge of the function of microbiomes and to predicting ecosystem responses to environmental change. Using natural forest soil samples from 110 locations, this study is one of the largest attempts to comprehensively understand the different patterns of soil archaeal, bacterial, and fungal biogeography at the continental scale in eastern China. These patterns in natural forest sites could ascertain reliable soil microbial biogeographic patterns by eliminating anthropogenic influences. This information provides guidelines for monitoring the belowground ecosystem’s decline and restoration. Meanwhile, the deviations in the soil microbial communities from corresponding natural forest states indicate the extent of degradation of the soil ecosystem. Moreover, given the association between vegetation type and the microbial community, this information could be used to predict the long-term response of the underground ecosystem to the vegetation distribution caused by global climate change. Author Video: An author video summary of this article is available.

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