scholarly journals Agricultural practice negatively affects soil microbial diversity and nitrogen functional genes comparing to adjacent native forest soils

2021 ◽  
Author(s):  
Tiehang Wu ◽  
Michael Sabula ◽  
Holli Milner ◽  
Gary Strickland ◽  
Gan Liu
Keyword(s):  
Community Structure ◽  
Bacterial Diversity ◽  
Forest Soils ◽  
Agricultural Practices ◽  
Functional Genes ◽  
Agricultural Practice ◽  
Soil Bacterial Diversity ◽  
Soil Microbial Diversity ◽  
Soil Microbial ◽  
Soil Bacterial

Soil microbial diversity and community are determined by anthropogenic activities and environmental conditions, which greatly affect the functioning of ecosystem. We investigated the soil bacterial diversity, communities, and nitrogen (N) functional genes with different disturbance intensity levels from crop, transition, to forest soils at three locations in the coastal region of Georgia, USA. Illumina high-throughput DNA sequencing based on bacterial 16S rRNA genes were performed for bacterial diversity and community analyses. Nitrifying (AOB amoA) and denitrifying (nirK) functional genes were further detected using quantitative PCR (qPCR) and Denaturing Gradient Gel Electrophoresis (DGGE). Soil bacterial community structure determined by Illumina sequences were significantly different between crop and forest soils (p < 0.01), as well as between crop and transition soils (p = 0.01). However, there is no difference between transition and forest soils. Compared to less disturbed forest, agricultural practice significantly decreased soil bacterial richness and Shannon diversity. Soil pH and nitrate contents together contributed highest for the observed different bacterial communities (Correlations = 0.381). Two OTUs (OTU5, OTU8) belonging to Acidobacteriales species decreased in crop soils, however, agricultural practices significantly increased an OTU (OTU4) of Nitrobacteraceae. The relative abundance of AOB amoA gene was significantly higher in crop soils than in forest and transition soils. Distinct grouping of soil denitrifying bacterial nirK communities was observed and agricultural practices significantly decreased the diversity of nirK gene compared to forest soils. Anthropogenic effects through agricultural practices negatively affecting the soil bacterial diversity, community structure, and N functional genes.

scholarly journals Agricultural practice altering soil microbial diversity and nitrogen functional genes comparing to adjacent native forest soils

2021 ◽  
Author(s):  
Tiehang Wu ◽  
Michael Sabula ◽  
Holli Milner ◽  
Gary Strickland ◽  
Gan Liu
Keyword(s):  
Community Structure ◽  
Bacterial Diversity ◽  
Forest Soils ◽  
Agricultural Practices ◽  
Functional Genes ◽  
Agricultural Practice ◽  
Soil Bacterial Diversity ◽  
Soil Microbial Diversity ◽  
Soil Microbial ◽  
Soil Bacterial

Soil microbial diversity and community are determined by anthropogenic activities and environmental conditions, which greatly affect the functioning of ecosystem. We investigated the soil bacterial diversity, communities, and nitrogen (N) functional genes with different disturbance intensity levels from crop, transition, to forest soils at three locations in the coastal region of Georgia, USA. Illumina high-throughput DNA sequencing based on bacterial 16S rRNA genes were performed for bacterial diversity and community analyses. Nitrifying (AOB amoA) and denitrifying (nirK) functional genes were further detected using quantitative PCR (qPCR) and Denaturing Gradient Gel Electrophoresis (DGGE). Soil bacterial community structure determined by Illumina sequences were significantly different between crop and forest soils (p < 0.01), as well as between crop and transition soils (p = 0.01). However, there is no difference between transition and forest soils. Compared to less disturbed forest, agricultural practice significantly decreased soil bacterial richness and Shannon diversity. Soil pH and nitrate contents together contributed highest for the observed different bacterial communities (Correlations = 0.381). Two OTUs (OTU5, OTU8) belonging to Acidobacteriales species decreased in crop soils, however, agricultural practices significantly increased an OTU (OTU4) of Nitrobacteraceae. The relative abundance of AOB amoA gene was significantly higher in crop soils than in forest and transition soils. Distinct grouping of soil denitrifying bacterial nirK communities was observed and agricultural practices significantly decreased the diversity of nirK gene compared to forest soils. Anthropogenic effects through agricultural practices negatively affecting the soil bacterial diversity, community structure, and N functional genes.

scholarly journals TRFLP Analysis of the Effect of a Forest-to-Gap Ectone on Soil Microbial Diversity

2014 ◽  
Author(s):  
Ronald Smith
Keyword(s):  
Microbial Diversity ◽  
Bacterial Diversity ◽  
Rrna Genes ◽  
Rrna Gene ◽  
Restriction Enzyme Digestion ◽  
Dna Fragments ◽  
Soil Bacterial Diversity ◽  
Soil Microbial Diversity ◽  
Soil Microbial ◽  
Soil Bacterial

<p>To investigate how soil microbial diversity is influenced by the formation of an experimental edge-creating gap within a southern New England oak-hickory forest, I used a molecular fingerprinting technique known as terminal restriction fragment length polymorphism (TRFLP). Sequence variability in the 16S ribosomal RNA (rRNA) gene in soil bacterial communities is detected by differences in the length and abundance of fragments produced by digesting PCR products amplified from rRNA genes. The different patterns observed are assumed to represent unique phylotypes.</p> <p>How does the forest-gap ecotone influence soil bacterial diversity? Based on other studies, I hypothesized that the edge would contain the most diverse bacterial community, followed by the gap, and as distance from the gap into the forest increased, bacterial diversity would decrease.</p> <p>Soil samples were collected along 40m transects perpendicular to the northern edge of the gap. DNA was extracted from each sample, PCR was used to amplify the 16S rRNA gene, and DNA fragments were cut by restriction enzyme digestion and separated via electrophoresis. The DNA fragments were analyzed by TRFLP.</p> <p>Environmental variables (soil pH, soil temperature and soil gravimetric moisture) were different in the gap compared to all other distances, but not significantly so. Phylotype richness and diversity (Simpson’s index) was greatest at the edge. Canonical Correspondence Analysis (CCA) produced a phylotype-by-distance ordination that supports my hypothesis and shows that the edge is an ecotone (transitional zone) between the gap and forest.</p>

scholarly journals Phosphorus Reduces Negative Effects of Nitrogen Addition on Soil Microbial Communities and Functions

2020 ◽  
Vol 8 (11) ◽  
pp. 1828 ◽  
Author(s):  
Zongwei Xia ◽  
Jingyi Yang ◽  
Changpeng Sang ◽  
Xu Wang ◽  
Lifei Sun ◽  
...  
Keyword(s):  
Microbial Communities ◽  
Bacterial Diversity ◽  
Soil Microbial Communities ◽  
N Deposition ◽  
N Fixation ◽  
N Addition ◽  
Soil Bacterial Diversity ◽  
Soil Microbial ◽  
Soil Bacterial ◽  
P Addition

Increased soil nitrogen (N) from atmospheric N deposition could change microbial communities and functions. However, the underlying mechanisms and whether soil phosphorus (P) status are responsible for these changes still have not been well explained. Here, we investigated the effects of N and P additions on soil bacterial and fungal communities and predicted their functional compositions in a temperate forest. We found that N addition significantly decreased soil bacterial diversity in the organic (O) horizon, but tended to increase bacterial diversity in the mineral (A) horizon soil. P addition alone did not significantly change soil bacterial diversity but mitigated the negative effect of N addition on bacterial diversity in the O horizon. Neither N addition nor P addition significantly influenced soil fungal diversity. Changes in soil microbial community composition under N and P additions were mainly due to the shifts in soil pH and NO3− contents. N addition can affect bacterial functional potentials, such as ureolysis, N fixation, respiration, decomposition of organic matter processes, and fungal guilds, such as pathogen, saprotroph, and mycorrhizal fungi, by which more C probably was lost in O horizon soil under increased N deposition. However, P addition can alleviate or switch the effects of increased N deposition on the microbial functional potentials in O horizon soil and may even be a benefit for more C sequestration in A horizon soil. Our results highlight the different responses of microorganisms to N and P additions between O and A horizons and provides an important insight for predicting the changes in forest C storage status under increasing N deposition in the future.

scholarly journals Regulating soil bacterial diversity, community structure and enzyme activity using residues from golden apple snails

2020 ◽  
Vol 10 (1) ◽  
Author(s):  
Jiaxin Wang ◽  
Xuening Lu ◽  
Jiaen Zhang ◽  
Guangchang Wei ◽  
Yue Xiong
Keyword(s):  
Community Structure ◽  
Bacterial Community ◽  
Bacterial Diversity ◽  
Soil Nutrients ◽  
Pomacea Canaliculata ◽  
Soil Bacterial Diversity ◽  
Amended Soils ◽  
Soil Bacterial ◽  
The Impact ◽  
Amended Soil

Abstract It has been shown that the golden apple snail (GAS, Pomacea canaliculata), which is a serious agricultural pest in Southeast Asia, can provide a soil amendment for the reversal of soil acidification and degradation. However, the impact of GAS residue (i.e., crushed, whole GAS) on soil bacterial diversity and community structure remains largely unknown. Here, a greenhouse pot experiment was conducted and 16S rRNA gene sequencing was used to measure bacterial abundance and community structure in soils amended with GAS residue and lime. The results suggest that adding GAS residue resulted in a significant variation in soil pH and nutrients (all P < 0.05), and resulted in a slightly alkaline (pH = 7.28–7.75) and nutrient-enriched soil, with amendment of 2.5–100 g kg−1 GAS residue. Soil nutrients (i.e., NO3-N and TN) and TOC contents were increased (by 132–912%), and some soil exocellular enzyme activities were enhanced (by 2–98%) in GAS residue amended soil, with amendment of 1.0–100 g kg−1 GAS residue. Bacterial OTU richness was 19% greater at the 2.5 g kg−1 GAS residue treatment than the control, while it was 40% and 53% lower at 100 g kg−1 of GAS residue and 50 g kg−1 of lime amended soils, respectively. Firmicutes (15–35%) was the most abundant phylum while Bacterioidetes (1–6%) was the lowest abundant one in GAS residue amended soils. RDA results suggest that the contents of soil nutrients (i.e., NO3-N and TN) and soil TOC explained much more of the variations of bacterial community than pH in GAS residue amended soil. Overuse of GAS residue would induce an anaerobic soil environment and reduce bacterial OTU richness. Soil nutrients and TOC rather than pH might be the main factors that are responsible for the changes of bacterial OTU richness and bacterial community structure in GAS residue amended soil.

scholarly journals Cover Cropping Impacts Soil Microbial Communities and Functions in Mango Orchards

Agriculture ◽  
2021 ◽  
Vol 11 (4) ◽  
pp. 343
Author(s):  
Zhiyuan Wei ◽  
Quanchao Zeng ◽  
Wenfeng Tan
Keyword(s):  
Bacterial Diversity ◽  
Fungal Diversity ◽  
Soil Microbial Communities ◽  
Soil Bacterial Diversity ◽  
Mango Fruit ◽  
Soil Biodiversity ◽  
Soil Microbial ◽  
Cover Cropping ◽  
Soil Bacterial ◽  
Soil Fungal Diversity

Soil microbes play critical roles in nutrient cycling, net primary production, food safety, and climate change in terrestrial ecosystems, yet their responses to cover cropping in agroforestry ecosystems remain unknown. Here, we conducted a field experiment to assess how changes in cover cropping with sown grass strips affect the fruit yields and quality, community composition, and diversity of soil microbial taxa in a mango orchard. The results showed that two-year cover cropping increased mango fruit yields and the contents of soluble solids. Cover cropping enhanced soil fungal diversity rather than soil bacterial diversity. Although cover cropping had no significant effects on soil bacterial diversity, it significantly influenced soil bacterial community compositions. These variations in the structures of soil fungal and bacterial communities were largely driven by soil nitrogen, which positively or negatively affected the relative abundance of both bacterial and fungal taxa. Cover cropping also altered fungal guilds, which enhanced the proportion of pathotrophic fungi and decreased saprotrophic fungi. The increase in fungal diversity and alterations in fungal guilds might be the main factors to consider for increasing mango fruit yields and quality. Our results indicate that cover cropping affects mango fruit yields and quality via alterations in soil fungal diversity, which bridges a critical gap in our understanding of the linkages between soil biodiversity and fruit quality in response to cover cropping in orchard ecosystems.

scholarly journals Identifying the Biogeographic Patterns of Rare and Abundant Bacterial Communities Using Different Primer Sets on the Loess Plateau

2021 ◽  
Vol 9 (1) ◽  
pp. 139
Author(s):  
Quanchao Zeng ◽  
Shaoshan An
Keyword(s):  
Community Structure ◽  
Environmental Factors ◽  
Bacterial Community ◽  
Bacterial Diversity ◽  
Bacterial Communities ◽  
Land Uses ◽  
The Loess Plateau ◽  
Soil Bacterial Diversity ◽  
Soil Bacterial ◽  
Rare Bacteria

High-throughput sequencing is commonly used to study soil microbial communities. However, different primers targeting different 16S rRNA hypervariable regions often generate different microbial communities and result in different values of diversity and community structure. This study determined the consequences of using two bacterial primers (338f/806r, targeting the V3-V4 region, and 520f/802r, targeting the V4 region) to assess bacterial communities in the soils of different land uses along a latitudinal gradient. The results showed that the variations in the soil bacterial diversity in different land uses were more evident based on the former pair. The statistical results showed that land use had no significant impact on soil bacterial diversity when primer pair 520f/802r was used. In contrast, when primer pair 338f/806r was used, the cropland and orchard soils had significantly higher operational taxonomic units (OTUs) and Shannon diversity index values than those of the shrubland and grassland soils. Similarly, the soil bacterial diversity generated by primer pair 338f/806r was significantly impacted by mean annual precipitation, soil total phosphorus (TP), soil total nitrogen (TN), and soil available phosphorus (AVP), while the soil bacterial diversity generated by primer pair 520f/802r showed no significant correlations with most of these environmental factors. Multiple regression models indicated that soil pH and soil organic carbon (SOC) shaped the soil bacterial community structure on the Loess Plateau regardless of what primer pair was used. Climatic conditions mainly affected the diversity of rare bacteria. Abundant bacteria are more sensitive than rare bacteria to environmental changes. Very little of the variation in the rare bacterial community was explained by environmental factors or geographic distance, suggesting that the communities of rare bacteria are unpredictable. The distributions of the abundant taxa were mainly determined by variations in environmental factors.

scholarly journals How Do Soil Bacterial Diversity and Community Composition Respond under Recommended and Conventional Nitrogen Fertilization Regimes?

2020 ◽  
Vol 8 (8) ◽  
pp. 1193
Author(s):  
Sami Ullah ◽  
Ping He ◽  
Chao Ai ◽  
Shicheng Zhao ◽  
Wencheng Ding ◽  
...  
Keyword(s):  
Community Structure ◽  
Bacterial Diversity ◽  
Community Composition ◽  
Crop Yield ◽  
Black Soil ◽  
N Fertilization ◽  
Partial Least Square ◽  
Least Square ◽  
Soil Bacterial Diversity ◽  
Soil Bacterial

Shifts in soil bacterial diversity and community composition are suggested to be induced by elevated input of nitrogen (N) fertilization with implications for soil quality, and consequently production. In this study, we evaluated the impacts of recommended fertilization (RF) and conventional fertilization (CF) on soil chemical properties, crop yield, bacterial diversity, and community composition from two long-term experiments conducted in fluvo-aquic soil and black soil of China. Each site comprised of four treatments, i.e., RF N−, RF N+, CF N−, CF N+. No N fertilization was indicated by N− and N fertilization was indicated by N+. Across both sites, N fertilization significantly increased crop yield compared with no N fertilization and RF successfully enhanced crop yield over CF. Interestingly, the RF maintained bacterial diversity, while CF depressed bacterial diversity in the two soils. Microbial taxa performing important ecological roles such as order Rhodospirillales and Bacillales were significantly enhanced in the RF approach, while Rhizobiales declined under CF. Furthermore, the results of partial least square path modeling revealed that soil available phosphorus (AP) negatively affected bacterial diversity while it positively affected bacterial community structure in fluvo-aquic soils. In contrast, soil pH was positively linked with both bacterial diversity and community structure in black soil. Overall, our study demonstrated that RF is an environmentally friendly approach which not only maintained above ground plant productivity, but also preserved belowground microbial populations and important soil variables regulating bacterial communities varied in different soil types.

scholarly journals Soil Bacterial Diversity and Productivity of Coffee - Shade Tree Agro-ecosystems

2012 ◽  
Vol 17 (2) ◽  
pp. 181 ◽  
Author(s):  
Rusdi Evizal ◽  
. Tohari ◽  
Irfan Dwidja Prijambada ◽  
Jaka Widada ◽  
Donny Widianto
Keyword(s):  
Bacterial Diversity ◽  
Soil Bacteria ◽  
Coffee Bean ◽  
Soil Bacterial Diversity ◽  
Soil Microbial Diversity ◽  
Organic C ◽  
Shade Coffee ◽  
Bean Yield ◽  
Soil Bacterial ◽  
Positive Effect

Coffee productions should have environmental value such as providing high soil microbial diversity while producing high yield. To examine that purposes, two experimental plots were constucted at benchmark site of Conservation and Sustainable Management of Below-Ground Biodiversity (CSM-BGBD), in Sumberjaya Subdistrict, West Lampung, Indonesia, during 2007-2010. Types of coffee agro-ecosystem to be examined were Coffea canephora with shade trees of Gliricidia sepium, Erythrina sububrams, Michelia champaca, and no shade. Two plots were constructed at 5-years-coffee and 15-years-coffee. Diversity of soil bacteria was determined based on DNA finger printing of total soil bacteria using Ribosomal Intergenic Spacer Analysis (RISA) method. The results showed that: (1) For mature coffee (15 years old), shade-grown coffee agro-ecosystems had higher soil bacterial diversity than those of no shade coffee agro-ecosystem, (2) Shaded coffee agro-ecosystems were able to conserve soil bacterial diversity better than no-shade coffee agro-ecosystem. Soil organic C and total litter biomass had positive effect on soil bacterial diversity, (3) Types of agro-ecosystem significantly affect the bean yield of 15 years coffee. Coffee agro-ecosystems shaded by legume trees had higher yield than those of non-legume shade and no shade coffee agro-ecosystem, (4) Shannon-Weaver indices of soil bacterial diversity together with weed biomass and N content of coffee leaf had positive effect on coffee bean yield.

scholarly journals History Leaves Its Mark on Soil Bacterial Diversity

mBio ◽  
2016 ◽  
Vol 7 (3) ◽  
Author(s):  
Jennifer B. H. Martiny
Keyword(s):  
Climate Change ◽  
Microbial Diversity ◽  
Bacterial Diversity ◽  
Soil Bacteria ◽  
Future Climate Change ◽  
Soil Bacterial Diversity ◽  
Soil Microbial Diversity ◽  
Climate Conditions ◽  
Soil Microbial ◽  
Evolutionary Diversification

ABSTRACT Dispersal is closely tied to the origin and maintenance of microbial diversity. With its focus on a narrow group of soil bacteria, recent work by Andam and colleagues on Streptomyces has provided perhaps the strongest support so far that some bacterial diversity in soils can be attributed to regional endemism (C. P. Andam et al., mBio 7:e02200-15, 2016, http://dx.doi.org/10.1128/mBio.02200-15 ). This means that dispersal is limited enough to allow for evolutionary diversification. Further analyses suggest that signatures of climate conditions more than 10,000 years ago can be detected in contemporary populations of this genus. These legacies have implications for how future climate change might alter soil microbial diversity.

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