Diversity Of Soil Microbial Communities Research Articles

Short-term application of chicken manure under different nitrogen rates alters structure and co-occurrence pattern but not diversity of soil microbial community in wheat field.

Manure application is an effective way to improve the utilization efficiency of organic resources and alleviate the adverse effects of long-term application of chemical fertilizers. However, the impact of applying manure under different nitrogen rates on soil microbial community in wheat field remains unclear. Treatments with and without chicken manure application under three nitrogen rates (N 135, 180 and 225 kg⋅hm–2) were set in wheat field. Soil organic carbon, available nutrients, and abundance, diversity, structure and co-occurrence pattern of soil microbial community at wheat maturity were investigated. Compared with no manure application, chicken manure application increased the soil organic carbon and available phosphorus, while the effects on soil mineral nitrogen and available potassium varied with different nitrogen rates. Chicken manure application significantly increased soil bacterial abundance under the nitrogen fertilization of 135 and 225 kg⋅hm–2, increased soil fungal abundance under the nitrogen fertilization of 135 kg⋅hm–2, but decreased soil fungal abundance under the nitrogen fertilization of 180 and 225 kg⋅hm–2 (P < 0.05). There was no significant difference in alpha diversity indices of soil microbial communities between treatments with and without chicken manure application under different nitrogen rates (P > 0.05). Chicken manure application and its interaction with nitrogen rate significantly changed soil bacterial and fungal community structures (P < 0.05). There were significantly different taxa of soil microbial communities between treatments with and without chicken manure application. Chicken manure application reduced the ecological network complexity of soil bacterial community and increased that of soil fungal community. In summary, the responses of soil available nutrients and microbial abundance to applying chicken manure varied with different nitrogen rates. One growing season application of chicken manure was sufficient to alter the soil microbial community structure, composition and co-occurrence pattern, whereas not significantly affected soil microbial community diversity.

Responses of soil microbial communities to concentration gradients of antibiotic residues in typical greenhouse vegetable soils

To explore the responses of soil microbial communities to concentration gradients of antibiotic residues in soil, 32 soil samples were collected from a typical greenhouse vegetable production base in Northern China in 2019. The total concentrations of 26 antibiotic residues in these soil samples was 83.24–4237.93 μg·kg−1, of which metabolites of tetracyclines were 23.34–1798.80 μg·kg−1. The total concentrations in 32 samples were clustered into three levels (L: <100 μg·kg−1, M: 100–300 μg·kg−1, H: >300 μg·kg−1) to elucidate the impacts of antibiotic residues on the diversity, structure, composition, function and antibiotic resistome of soil microbial community. Results showed that higher concentration of antibiotic residues in soil was prone to decrease the diversity and shift the structure and composition of soil microbial community. Antibiotic resistome occurred in soils with antibiotic residues exceeding 300 μg·kg−1. Interactions among soil bacteria followed the order of H > L > M, consistent with the relative abundances of mobile genetic elements. Bacteroidetes and Firmicutes were the top attributors impacting the profile of antibiotics in soil. According to weighted comprehensive pollution index of risk quotient, in 28.1 % of soil samples the residual antibiotics presented high ecological risk, whereas in the rest of soil samples the ecological risk is medium. The results will enrich the database and provide references for antibiotic contamination control in soils of the region and alike.

Tillage intensity and plant rhizosphere selection shape bacterial-archaeal assemblage diversity and nitrogen cycling genes

Agroecosystem management practices, plant-microbe interactions, and climate are all factors that influence soil microbial community diversity and functionality. Herein, we assessed diversity of soil bacterial-archaeal assemblages and denitrification gene markers in a long-term tillage field experiment. We evaluated bulk and rhizosphere soils from two crop years (corn and soybean) of a three-year rotation of corn-soybean-small grain + cover crop. Soil samples were collected at three growth stages from corn and soybean plants and across three tillage practices that had been applied every year for 40 years. Tillage practices represented three levels of disturbance intensity ranging from low (no-till) to intermediate (chisel-disk) to high (moldboard plow) intensities. Bacterial assemblage diversity differed in soils having contrasting tillage histories and from bulk or rhizosphere soil (compartments), crop year, and growth stage. Compared to plowed and chisel-disked soils, no-till soils had lower abundances of denitrification genes, higher abundances of genes for dissimilatory nitrate reduction to ammonium (DNRA), and higher abundances of family-level taxa associated with archaeal nitrification and anammox. Soybean rhizospheres exerted stronger selection on bacterial-archaeal composition and diversity relative to corn rhizospheres. Abundances of N genes were grouped by factors related to weather, as well as management and soil compartment, which could impact activity related to denitrification and DNRA. Low intensity tillage may provide an option to reduce potential ‘hot spots’ or ‘hot moments’ for N losses in agricultural soils, although weather and crop type are also important factors that can influence how tillage affects microbial assemblages and microbial N use.

Effects of Land Conversion on Soil Microbial Community Structure and Diversity in Songnen Plain, Northeast China

To feed the growing human population, natural grasslands are being converted to agricultural use at a massive scale. This conversion may have consequences for soil biodiversity, but its impact on the community assembly of differentially microbial groups remains largely unknown. Here, we selected the three typical land-use types: grassland, arable land (formerly grassland), and forest (formerly grassland) in the Songnen Plain, Northeastern China. Illumina MiSeq high-throughput sequencing technology based on bacterial 16S rRNA and fungal ITS rRNA was used to study the community structures and diversities of soil bacteria and fungi and to explore the drivers of these changes. The results showed that bacterial community diversity did not change after grassland conversion to forest and arable land, but affected bacterial community abundance at the phylum level. Actinomycetes and Proteobacteria were significantly reduced, Acidobacteria were significantly increased, and Gemmatimonadetes and Bacteroidetes were the most abundant in arable land. Land conversion had significant effects on both fungal community diversity and abundance. After the grassland was converted into forest, the fungal community diversity decreased, but the community abundance increased significantly, the Ascomycetes decreased significantly, and Basidiomycetes became the dominant phylum, especially white rot fungi. Interestingly, the fungal community diversity and community abundance increased significantly after grassland was converted to arable land, and the abundance of Zygomycota increased significantly but the dominant phylum was still Ascomycetes. Canonical correlation analysis (CCA) showed pH, MC, NO3−-N, TP, AP, and other soil factors are important factors affecting the composition of microbial communities. In the soil of this study area, the composition of bacterial communities is mainly driven by changes in pH and soil texture, and the composition of fungal communities is most closely related to changes in soil nutrient utilization. Changes in land-use patterns have an effect on the structure and diversity of microbial communities by changing the physical and chemical properties of the soil.

Effect of H3PO4-modified biochar on the fate of atrazine and remediation of bacterial community in atrazine-contaminated soil

The application of chemically modified biochar is a promising strategy for the remediation of contaminated (e.g., pesticides) soil. In this study, H3PO4 was used to modify peanut shell to improve the remediation performance of biochar. Surface area (980.19 m2/g), pore volume (0.12 cm3/g), and the functional groups (OH, CO, and phosphorus-containing groups) on the biochar were increased by H3PO4 treatment. The sorption experimental data were well fitted by Freundlich model, while the sorption affinity (Kf) of H3PO4 modified biochar (PBC) for atrazine was 128 times greater than that of the untreated biochar (BC) in the aquatic systems. The Kf values of PBC-amended soil to atrazine were increased by 13.57 times than that of single soil. The strong sorption of PBC on atrazine delayed the degradation of atrazine in soil, and the residual percentage of atrazine in soil and soil-PBC mixture were 4.90% and 71.44% at the end of 60-day incubation, with the degradation half-life increased from 13.3 to 121.6 d. The analysis of high-throughput sequencing results showed that atrazine reduced the diversity of soil microbial community, but the abundance of microorganisms with degradation function increased and became dominant species. The addition of PBC in soil accelerated the microbial remediation of atrazine stress, which may promote the soil nitrogen cycle. Therefore, amendment of atrazine contaminated soil with PBC can reduce the environmental risk of atrazine and benefit the soil microbial ecology.

Microbial mechanism of zinc fertilizer input on rice grain yield and zinc content of polished rice.

Zinc is an essential minor element for rice growth and human health, which can also change the structure of the microorganisms. However, it remains unclear for the effects of zinc fertilizer on microbiome function in agricultural soils and crops. To solve this research gap, we investigated the relationship between improving rice (Oryza sativa L.) yield, Zn concentration, soil microbial community diversity, and function by the application of Zn fertilizer. The field trials included three rice varieties (Huanghuazhan, Nanjing9108, and Nuodao-9925) and two soil Zn levels (0 and 30 kg ha–1) in Jiangsu province, China. As a test, we studied the variety of soil bacterial composition, diversity, and function using 16S rRNA gene sequencing. The results showed that soil Zn application reduced the diversity of microbial community, but the bacterial network was more closely linked, and the metabolic function of bacterial community was improved, which increased the grain yield (17.34–19.52%) and enriched the Zn content of polished rice (1.40–20.05%). Specifically, redundancy analysis (RDA) and Mantel’s test results revealed soil total nitrogen (TN) was the primary driver that led to a community shift in the rice rhizosphere bacterial community, and soil organic carbon (SOC) was considered to have a strong influence on dominant phyla. Furthermore, network analysis indicated the most critical bacterial taxa were identified as Actinobacteria, Bacteroidetes, Proteobacteria, and Chloroflexi based on their topological roles of microorganisms. KEGG metabolic pathway prediction demonstrated that soil Zn application significantly (p < 0.05) improved lipid metabolism, amino acid metabolism, carbohydrate metabolism, and xenobiotic biodegradation. Overall, their positive effects were different among rice varieties, of which Nanjing-9108 (NJ9108) performed better. This study opens new avenues to deeply understand the plant and soil–microbe interactions by the application of fertilizer and further navigates the development of Zn-rich rice cultivation strategies.

Effects of Intercropping between Morus alba and Nitrogen Fixing Species on Soil Microbial Community Structure and Diversity

The intercropping of nitrogen-fixing and non-nitrogen-fixing tree species changed the availability of soil nitrogen and soil microbial community structure and then affected the regulation process of soil carbon and nitrogen cycle by microorganisms in an artificial forest. However, there is no consensus on the effect of soil nitrogen on soil microorganisms. In this study, the intercropping of mulberry and twigs was completed through pot experiments. Total carbon, total nitrogen, and total phosphorus in the rhizosphere soil were determined, and the composition and structure of the soil microbial community were visualized by PCR amplification and 16S rRNA ITS sequencing. The analysis found that the intercropping of Morus alba L. and Lespedeza bicolor Turcz. had no significant effect on soil pH but significantly increased the contents of total carbon, total nitrogen, and total phosphorus in the soil. The effect on the alpha diversity of the bacterial community was not significant, but the effect on the evenness and diversity of the fungal community was significant (p &lt; 0.05). It was also found that soil nutrients had no significant effect on bacterial community composition but had a significant effect on the diversity within the fungal community. This study added theoretical support for the effects of intercropping between non-nitrogen-fixing tree species and nitrogen-fixing tree species on soil nutrients and microbial community diversity.

Advances in the Effects of Biochar on Microbial Ecological Function in Soil and Crop Quality

Biochar, a late-model environmental functional material, has been widely applied in environmental remediation, agricultural production, and energy utilization due to its excellent characteristics such as porosity and high specific surface area. In recent years, many studies on the effects of biochar on agricultural soil and crop quality have been performed. The application of biochar can influence soil microbial status directly or indirectly by changing the physicochemical properties of soil. Apart from increasing soil pH, biochar can also increase soil organic matter and nutrient elements, which ultimately affect crop yield and quality. This review summarizes and overviews the recent research advances on the influence of biochar application on soil microbial community diversity, microbial ecological functions, soil enzymes and their functional genes, and on crop quality and yield from the perspective of soil microorganisms. This review provides guidance and references for further research into biochar applications.

Soil Microbial Diversity and Community Composition in Rice-Fish Co-Culture and Rice Monoculture Farming System.

Simple SummaryThe integration of fish in rice fields can influence the diversity and structural composition of soil microbial communities. Therefore, soil microorganisms between rice–fish co-culture (RF) and rice monoculture (MC) were compared. The key findings revealed that Actinobacteria, Chloroflexi, Proteobacteria, Acidobacteria, and Planctomycetes were the most dominant taxa across both paddy fields. The most abundant genus in MC belonged to Anaeromyxobacter, whereas that in RF was Bacillus. Nitrogen fixation, aromatic compound degradation, and hydrocarbon degradation were more abundant in RF. Phosphatase, β-glucosidase, cellulase, and urease enzymes were detected in both paddy fields. However, a 2-year conversion from organic rice to rice–fish co-culture may not be long enough to significantly alter alpha diversity indices.Soil microorganisms play an important role in determining nutrient cycling. The integration of fish into rice fields can influence the diversity and structural composition of soil microbial communities. However, regarding the rice–fish co-culture (RF) farming system in Thailand, the study of the diversity and composition of soil microbes is still limited. Here, we aim to compare the microbial diversity, community composition, and functional structure of the bacterial communities between RF and rice monoculture (MC) farming systems and identify the environmental factors shaping bacterial community composition. Bacterial taxonomy was observed using 16s rRNA gene amplicon sequencing, and the functional structures of the bacterial communities were predicted based on their taxonomy and sequences. The results showed that soil organic carbon, total nitrogen (TN), organic matter, available phosphorous, and clay content were significantly higher in RF than in MC. The most dominant taxa across both paddy rice fields belonged to Actinobacteria, Chloroflexi, Proteobacteria, Acidobacteria, and Planctomycetes. The taxa Nitrosporae, Rokubacteria, GAL15, and Elusimicrobia were significantly different between both rice fields. At the genus level, Bacillus, Anaeromyxobacter, and HSB OF53-F07 were the predominant genera in both rice fields. The most abundant genus in MC was Anaeromyxobacter, whereas RF belonged to Bacillus. The community composition in MC was positively correlated with magnesium and sand content, while in RF was positively correlated with pH, TN, and clay content. Nitrogen fixation, aromatic compound degradation, and hydrocarbon degradation were more abundant in RF, while cellulolysis, nitrification, ureolysis, and phototrophy functional groups were more abundant in MC. The enzymes involved in paddy soil ecosystems included phosphatase, β-glucosidase, cellulase, and urease. These results provide novel insights into integrated fish in the paddy field as an efficient agricultural development strategy for enhancing soil microorganisms that increase soil fertility.

Effects of rape/common vetch intercropping on biomass, soil characteristics, and microbial community diversity

Legume–brassica intercropping is widely used to increase productivity in modern, sustainable agricultural systems. However, few studies have assessed the linkages between soil properties and soil microorganisms. Soil microorganisms play a key role in soil nutrient turnover and plant community composition. To elucidate the responses of soil microbial community diversity and structure to intercropping, we conducted a 2-year experiment based on common vetch (CV) monoculture, rape (R) monoculture, and common vetch–rape intercropping (IRCV) with phosphorus (P) addition in alkaline soil. The microbial communities of bacteria and fungi in the rhizosphere soil were examined based on high-throughput sequencing targeting the 16S rRNA and ITS genes, respectively. In addition, we analyzed changes in soil properties and enzyme activities. Intercropping significantly increased dry matter (up to 98.86% and 81.48%, respectively dry matter is the aboveground biomass.) compared with common vetch monoculture. Intercropping decreased soil bulk density and pH and enhanced soil available phosphorus (AP) by 14.54–34.38%, 7.25–22.67%, soil organic matter (SOM) by 15.57–22.85, 6.82–15.57%, soil sucrase (Suc.) by 13.69–16.10%, 35.57–40.24% compared to monoculture common vetch and rape, respectively. However, bacterial alpha diversity was higher under rape monoculture than IRCV. In addition, the dominant soil bacterial phyla Proteobacteria (1.25–3.60%), Gemmatimonadetes (7.88–15.16%), Bacteroidetes (9.39–11.76%), and Rokubacteria (0.49–5.69%) were present at greater abundance with IRCV relative to those with CV and R, but phyla Chloroflexi was significantly decreased by 11.56–12.94% with IRCV compared with the other two treatments. The redundant analysis showed that SOM and AP were positively correlated with the dominant bacterial and fungal flora. Common vetch–rape intercropping resulted in increased biomass and altered soil microbial community composition as well as soil properties. Our results showed that intercropping systems positively improve soil microbial activity; this strategy could help in the cultivation of multiple crops and improve soil properties through sustainable production.

A field study of nano-FeS loaded lignin hydrogel application for Cd reduction, nutrient enhancement, and microbiological shift in a polluted paddy soil

Cadmium (Cd) pollution in paddy soil has caused serious harm to human health. Nano-ferrous sulfide@lignin hydrogel (FeS@LH) composites could be an ideal material for paddy soil Cd removal due to the excellent adsorption performance and mechanical strength. But the FeS@LH’s performance in a paddy field remains unclear. In this study, FeS@LH was applied to a Cd-contaminated paddy field when planting water spinach (Ipomoea aquatica Forssk). The results showed that FeS@LH effectively removed Cd from the soil (37.6 %) and water spinach (34.5 %) after 30 days. The concentrations of Pb, Zn, Cu, and other metals in soil and water spinach were co-reduced. When the FeS@LH dosage was 30 g·m−2, the effective functional distance was within 30 cm. FeS@LH application had a positive effect on soil nutrients. The soil nitrogen and organic matter contents increased by 16.1 % and 13.8 %, respectively. No significant effect on soil total phosphorus and potassium contents was presented. The survival rate of zebrafish in the acute toxicity test of FeS@LH was 98.9 %, indicating its biosafety. In addition, FeS@LH application decreased soil microbial community diversity probably due to the decreased pH. The microbial metabolism tended to enhance, suggesting a restoration of soil microbial community function after Cd removal.

Altering microbial community for improving soil properties and agricultural sustainability during a 10-year maize-green manure intercropping in Northwest China

Maize is a crop that is cultivated worldwide. The Hexi Oasis is one of the most important areas for high-yield maize seed production in China. Green manure, a plant fertilizer, has great potential for increasing crop yield and agricultural sustainability. However, the role of microorganisms in soil health and the microbiological mechanism of green manure in improving soil fertility and crop production in the Hexi Oasis area remain unknown. The effects of maize–green manure intercropping on the soil microbial community structure and diversity and the mechanism of soil improvement were investigated in a 10-year field experiment. The study revealed that microbial phylotypes were grouped into four major ecological clusters. Module #2 is a soil core ecological cluster enriched with many plant growth-promoting rhizobacteria and arbuscular mycorrhizal fungi. The application of green manure led to significantly increased soil pH, nutrient contents, and enzyme activities, and significantly reduced the relative abundance of potential plant pathogens compared with monocropping, which should ensure high and stable maize yield under long-term continuous cropping. It also increased the economic benefits by 56.39% compared with monocropping, owing to the additional products produced by the green manure. These improvements were associated with changes in the microbial community structure and activity, consistent with the structural equation model results. Therefore, soil microorganisms are the key drivers of the potential benefits of maize-green manure on agricultural sustainability.

Study on Microbial Community Structure and Soil Nitrogen Accumulation in Greenhouse Vegetable Fields with Different Planting Years

Soil microbial communities are an important part of the soil ecosystem in greenhouse vegetable fields, where ammonia-oxidising microorganisms play a key role in nitrogen conversion. The health and stability of the ecological environment of greenhouse vegetable fields are affected by the number of years of continuous cultivation. We used real-time PCR amplification and 16S rRNA gene sequencing to analyse the changes in soil microbial community structure and diversity in different planting years (0, 3, 9, and 13). The content of environmental factors increased with the increase of planting year; the NO3−-N content in the 0–20 cm soil layer showed a cumulative trend, peaking to 1290–1390 mg/kg in year 13. The abundance of operational taxonomic units (OTUs) in the microbial community gradually decreased, and the OTUs of 0–20 cm soil layer in year 13 decreased by 52.2% compared to year 0. The Shannon and Simpson indices indicated a substantial decrease in microbial diversity after year 9. The dominant phyla in the soil microbial community mainly included Firmicutes (23.6%), Actinobacteria (23.2%), Proteobacteria (17.6%), Crenarchaeota (83.4%), and Euryarchaeota (2.7%). Nitrosopumilus and Nitrososphaera in the ammonia-oxidising archaeal (AOA) community and Nitrolancea and Nitrospira in the ammonia-oxidising bacterial (AOB) community dominated the ammonia-oxidising microorganisms. With the increase in planting years in greenhouse vegetable fields, the structure of soil microbial community changed significantly, with soil biomass and diversity significantly decreasing in years 9 and 13. Reasonable fertilization and planting year would improve microbial activity and provide a basis for sustainable utilization and high-quality production in greenhouse vegetable fields.

Variations of rhizosphere and bulk soil microbial community in successive planting of Chinese fir (Cunninghamia lanceolata).

Successive planting and monoculture, as common forest management methods, are widely used globally, especially in Chinese fir plantations in the subtropical areas of southern China. Although soil fertility depletion and productivity decline caused by successive planting have been widely reported, the underlying mechanism is still ambiguous. In this study, the composition and diversity of soil microorganisms (rhizosphere and bulk soils) in Chinese fir seedlings exposed to successive planting soils (first-generation Chinese fir seedings, FCP. second-generation Chinese fir seedings, SCP. third-generation Chinese fir seedings, TCP) and broadleaf tree species soil (Phoebe zhennan S. Lee et F. N. Wei, CK) were examined with high-throughput sequencing technology. Our findings revealed that the diversity and richness of bacterial and fungal communities were remarkably reduced in TCP than FCP and SCP, and were remarkably different between FCP and SCP. At the phylum level, the fungi with greatest relative abundance were Basidiomycota (5.74–32.88%) and Ascomycota (57.63–87.38%), while the bacteria with the greatest relative abundance were Acidobacteria (23.16–31.17%) and Proteobacteria (24.71–29.32%) for all treatments in both soil types. Additionally, the relative abundance of some pathogens (Penicillium and Burkholderia) was significantly higher in TCP than in FCP and SCP, suggesting that the presence of pathogens is an important factor in increasing the incidence of soil-borne sickness. Moreover, changes in fungal and bacterial communities were predominantly driven by soil dissolved organic carbon (DOC), DOC/DON ratio (DOCN), NO3–-N, microbial biomass carbon (MBC), and MBC/MBN ratio (MBCN). Overall, the long-term monoculture of Chinese fir promotes the microecological imbalance of rhizosphere and bulk soil, and remarkably reduced soil microbial community diversity. These results can provide a scientific support for the implementation of future management measures for fir plantations (e.g., fertilization, addition of microbial fungicides, and construction of mixed forests).

Unraveling consequences of the co-exposure of polyethylene microplastics and acid rain on plant-microbe-soil system

Emerging microplastics (MPs) pollution and continuing acid rain (AR) co-exist in terrestrial ecosystems, and are considered as threats to ecosystems health. However, few data are available on MPs-AR interactions in plant-microbe-soil systems. Here, a microcosm experiment was manipulated to elucidate the co-exposure of polyethylene MPs (PE MPs; 1%, 5% and 10%) and AR (pH 4.0) on soil-lettuce system, in which the properties of soil and lettuce, and their links were explored. We found that 10% PE MPs increased soil CO2 emission and its temperature sensitivity (Q10) in combination with AR, while 1% PE MPs reduced soil CO2 emission irrespective of AR. PE MPs addition did not influence lettuce production (total biomass) though its photosynthesis was affected. PE MPs exerted negative impact on soil water availability. PE MPs treatments increased NH4+-N content of soil without AR, and dissolved organic carbon content of soil sprayed with AR. 10% PE MPs combined with AR reduced soil microbial biomass, while soil microbial community diversity was not affected by PE MPs or AR. Interestingly, 10% PE MPs addition altered soil microbial community structure, and promoted the complexity and connectivity of soil microbial networks. 5% and 10% PE MPs addition decreased soil urease activity under AR, but this was not the case without AR. These findings highlight the critical role of AR in regulating PE MPs impacts on plant-microbe-soil ecosystems, and the necessity to incorporate other environmental factors when evaluating the actual impacts or risks of MPs pollution in terrestrial ecosystems.

Development of a soil quality index for sequences with different levels of land occupation using soil chemical, physical and microbiological properties

The sustainable intensification of agricultural systems through crop rotations and/or the use of winter service crops can contribute to the diversification of the systems. This alteration of the surface layer creates conditions that favor an increase in the diversity of soil microbial communities, which improves the recovery capacity of the edaphic system, thereby contributing beneficial effects to plants, soil, and ecosystem. Our objectives were: 1) to evaluate the effect of crops sequences on soil chemical, physical and microbial parameters, and 2) to develop a soil quality index (SQI) from a minimum set of indicators for cropping sequences with different levels of land occupation. A long field experiment under no-tillage was established in 2006, where soil samples were collected during three agricultural seasons (2015, 2016, and 2017). We compared the effects of four different crop sequences that included soybean (S), maize (M) and wheat (W), and also incorporated wheat as a winter cover crop (CC), being S-S, CC/S, M-W/S, and W/S-CC/M. We found that sustainable management practices, crop rotation and inclusion of CC increased soil organic carbon. The highest basic infiltration rate and lowest penetration resistance values were found for double-cropped wheat/soybean-winter cover crop/maize (W/S-CC/M), the most intensified sequence. The average microbial biomass carbon level for soybean monoculture, was reduced by 32 % compared to maize-double-cropped wheat/soybean in the three agricultural seasons, while the metabolic coefficient in soybean monoculture and winter cover crop/soybean was significantly higher. In soybean monoculture, hydrolysis of fluorescein diacetate was decreased by 28.5 %, while dehydrogenase activity was increased by 43 % with respect to double-cropped wheat/soybean-winter cover crop/maize. The abundance of fungal and bacterial communities did not reveal significant variations between sequences by quantitative PCR analysis. The SQI was constructed by selecting a minimum set of indicators based on soil chemical, physical and microbial parameters. The parameters selected by the model were soil organic carbon, total organic nitrogen, basic infiltration rate, microbial respiration and hydrolysis of fluorescein diacetate, that revealed the differences among crop sequences in response to land occupation. The inclusion of different crops increased the SQI in comparison with soybean monoculture. The double-cropped wheat/soybean-winter cover crop/maize system improved the SQI by 73 % compared to soybean monoculture. Our findings show that crop sequences with high soil occupation improved their chemical and physical properties, as well as increasing the abundance and functionality of the microbial community, which is related to a better SQI.

Alterations in soil microbial phospholipid fatty acid profile with soil depth following cropland conversion in karst region, southwest China.

The soil microbial community is a key indicator used to evaluate the effectiveness of land use changes in degraded ecosystems. However, there is currently limited information on the vertical variations of soil microbial communities under different cropland types in the karst region of southwest China. In this study, three different cropland types (sugarcane, mulberry, and forage grass) were selected to replace maize-soybean cultivation in a karst area of southwest China. Secondary forest was included for comparison. Soil was collected at soil depths of 0-10cm, 10-20cm, 20-30cm, and 30-50cm to conduct a phospholipid fatty acid (PLFA) analysis of the soil microbial communities. The results showed that the abundances of total PLFAs and PLFAs of bacteria, fungi, actinomycetes, and arbuscular mycorrhizal fungi were significantly higher in forage grass cultivation and secondary forest areas than those in other three cropland types. The abundance of total PLFA and its functional groups significantly decreased with increasing soil depth. Bacteria was the predominant community (> 52%) across all land use types and soil depths. A principal component analysis indicated that soil microbial PLFA composition in forage grass field and secondary forest areas differed significantly from that in mulberry, sugarcane, and maize-soybean fields across 0-50-cm soil layer. Soil organic carbon was identified as the primary factor affecting the abundance and structure of soil microbial communities in the four soil layers. These results suggest that greater improvements in soil quality and fertility could be made by replacing the maize-soybean rotation system with forage grass cultivation than by replacing it with mulberry or sugarcane cultivation in the karst region of southwest China.

Changes in physicochemical property and microbial community of Pseudostellaria heterophylla soil at diffe-rent fallow ages

Pseudostellaria heterophylla is authentic traditional Chinese herbal medicine in Fujian Province. P. hete-rophylla suffers from serious consecutive monoculture problems. Fallow can alleviate such problems, but the mecha-nism is still unclear. In this study, high-throughput sequencing was performed to analyze the changes in soil microbial community structure and diversity in the P. heterophylla soil at different fallow ages as well as their relationships with soil physicochemical properties and phenolic acids. The results showed that fungal community diversity decreased but bacterial community diversity increased in fallow soils compared with the control soil of P. heterophy-lla. For bacterial communities, the relative abundance of Acidobacteria increased, while that of Proteobacteria and Actinobacteria decreased in fallow soils. For fungal communities, the relative abundance of dominant phyla had no significant difference between fallow and control soils. Soil acidity and organic matter content showed a trend of weakening and decreasing, respectively, with the increases of fallow years. In addition, with the increases of fallow years, the content of phenolic acids in soil, including benzoic acid and salicylic acid, showed significant decrease, while some other phenolic acids such as p-coumaric acid were accumulated obviously. Taken together, fallow could efficiently ameliorate the structure of soil microbial community and soil properties of P. heterophylla, and thus alleviate the effects of continuous cropping.

Resilient Soils for Resilient Farms: An Integrative Approach to Assess, Promote, and Value Soil Health for Small- and Medium-Size Farms

Healthy soils are the foundation of our food system and support broad environmental goals, including improved water quality and carbon sequestration. Increasingly, we appreciate that aspects of soil health such as fertility for plants, suppression of disease, and cycling of nutrients are linked to the functional diversity of soil microbial communities. The impact of functional capacity is influenced by farm management, which varies with farm size. Small to medium-size farms, with gross sales of less than $250,00 per year, make up 89% of farms in the United States, despite often being ignored in policy decisions. They are often more integrated into local food systems than larger farms, have greater investment in long-term sustainability due to their tendency to be passed from farmers to children, and are more reliant on soil health than larger farms. We describe a research framework to advance understanding of the soil microbiome and its role in soil health, environmental outcomes, and agricultural sustainability on small and medium farms. Our perspective elevates four research priorities to link the benefits of healthy soil microbiomes from the microscale to the macroscale. We hope this approach will lead to practical applications to enable success in the context of ongoing environmental and economic challenges that affect the agricultural landscape.

Effects of land use on soil microbial community structure and diversity in the Yellow River floodplain

Abstract Soil microorganisms and their diversity are important bioindicators of soil carbon and nutrient cycling. Land use type is a major determining factor that influences soil microbial community composition in floodplain ecosystems. However, how the structure and diversity of soil microbial communities respond to specific changes in land use, as well as the main drivers of these changes, are still unclear. This study was conducted in the Yellow River floodplain to examine the effects of land use type on soil microbial communities. Four land use types (shrubland, farmland, grassland and forest) were selected, wherein shrubland served as the baseline. We measured soil microbial structure and diversity using phospholipid fatty acids (PLFAs). Land use type significantly affected total, bacterial and fungal PLFAs, and the gram-positive/negative bacterial PLFAs. Compared with shrubland, peanut farmland had higher total and bacterial PLFAs and forest had higher fungal PLFAs. Soil pH and phosphorus were the predominate drivers of microbial PLFAs, explaining 37% and 26% of the variability, respectively. Soil total nitrogen and nitrate nitrogen were the main factors increasing microbial community diversity. Peanut farmland had the highest soil carbon content, soil carbon stock, total PLFAs and microbial diversity, suggesting that farmland has great potential as a carbon sink. Our findings indicated that peanut farmland in the Yellow River floodplain is critical for maintaining soil microbial communities and soil carbon sequestration.