Soil Bacterial Alpha Diversity Research Articles

Succession of bacterial and fungal communities during the mud solarization of salt-making processing in a 1000-year-old marine solar saltern

A 1000-year-old marine solar saltern in Hainan Island, South China, is in the continuation of traditional skills involving mud soak and solarization for three days to accumulate salt, which is a unique process contributing to the selection of highly halophilic microbes related to salt quality and flavor. Herein, the successions of physicochemical properties and bacterial and fungal communities of muds from the saltern were investigated during the processing of mud solarization. The results showed that Na+, Cl−, Mg2+ and total nitrogen were the main factors in explaining the fluctuation of the fungal community, whereas the bacterial community was predominantly determined by Ca2+, total kalium and total phosphorus. During three days of mud solarization, the soil bacterial alpha diversity in the saltern was significantly lower than that of the surroundings, whereas the fungal alpha diversity showed an opposite trend. The bacterial functional groups with the same survival and adaptation strategies remained relatively stable, while the dominant functional type in fungi changed from monotropic to complex trophic mode. Additionally, some unidentified fungi species were increasingly found in mud. The abundances of Saitozyma, Solicoccozyma and Wallemia (Basidiomycota) increased and may contribute to the salt flavor through decomposing cellulose molecules into glucose due to their higher β-glucosidase activity, while the harmful fungal genera including Inocybe and Paraconiothyrium decreased obviously due to the stresses of salinity and solar exposure. These results showed that the traditional salt-making skills associated with mud solarization have selected a high abundance of beneficial halophilic microbes to increase the salt quality and flavor. Our findings not only reveal the underlying mechanisms for the long-history salt-making skills of this 1000-year-old unusual cultural heritage but also are highly valuable for bioprospecting to develop novel halophilic bacteria and fungi for modern chemistry industries.

Afforestation-Induced Shifts in Soil Bacterial Diversity and Community Structure in the Saihanba Region.

Afforestation plays a pivotal role in ecosystem restoration, exemplified by the Saihanba Mechanized Forest Farm, the world's largest planted forest; however, the assembly mechanisms and interactions of soil microbial communities in such forests remain inadequately understood. This study aimed to elucidate the impact of different afforestation tree species, namely Larix gmelinii var. principis-rupprechtii, Picea asperata, and Pinus sylvestris var. mongolica, on soil bacterial diversity and community structure in comparison to grassland. Sixty soil samples were collected at a 20 cm depth, and high-throughput sequencing was employed to identify bacterial communities and assess their interactions with environmental factors. A total of 6528 operational taxonomic units (OTUs) were identified, with Solirubrobacter, Conexibacter, Bacillus, Massilia, Gaiella, Acidibacter, and Vicinamibacter being the dominant genera. Afforestation significantly impacted soil bacterial alpha diversity, with notable influence from key soil chemical properties, including available phosphorus (AP), cation exchange capacity (CEC), and the carbon-to-nitrogen ratio of soil organic matter (SOM-C/N). The Mantel test highlighted pH, the Normalized Difference Vegetation Index (NDVI), and spatial variable (dbMEM) as primary environmental factors influencing dominant bacterial genera. The bacterial community structure demonstrated deterministic homogeneous selection, wherein SOM-C/N emerged as a significant factor influencing the dissimilarity of soil bacterial communities. Furthermore, plantation soils exhibited a more complex network structure than grassland soil, highlighting the crucial role of bacterial communities in vegetation changes and providing valuable insights into their response to environmental factors during the reforestation process.

Planting grass enhances relations between soil microbes and enzyme activities and restores soil functions in a degraded grassland.

Forage culture is a common way to restore degraded grasslands and soil functions, in which the reconstruction of the soil microbial community and its relationship with extracellular enzyme activity (EEAs) can characterize the recovery effects of degraded grasslands. However, the impacts of forage culture on the interaction between soil microbes and EEAs and whether the recovery effect of soil functions depends on the varying degradation statuses remain unclear. We conducted a plantation of a dominant grass, Leymus chinensis, in the soil collected from severe, moderate, light, and non-degradation statuses in the Songnen grassland in northeastern China. We measured soil microbial diversity and soil EEAs, and predicted microbial functional groups using FUNGuild. The results showed that L. chinensis culture promoted soil bacterial alpha diversity and soil EEAs only in the moderate degradation status, indicating a dramatic dependence of the recovery effects of the grass culture on degradation status of the grassland. After planting L. chinensis for 10 weeks, a decreasing trend in the chemoheterotrophy and nitrate-reduction microbial functional groups was found. In contrast, the abundance of the nitrogen (N)-fixing microbial functional group tended to increase. The positive correlation between soil EEAs and the nitrate-reduction and N-fixing microbial functional groups was enhanced by planting L. chinensis, indicating that grass culture could promote soil N cycle functions. We illuminate that grass culture may promote the restoration of soil functions, especially soil N cycling in degraded grasslands, and the recovery effect may depend on the grassland degradation status. We emphasized that selection of the plant species for restoration of grasslands needs to consider the restoration effects of microbial functional groups and soil functions.

Effects of hexabromocyclododecane and polyethylene microplastics on soil bacterial communities

Hexabromocyclododecane (HBCD) and polyethylene (PE) microplastic are ubiquitous pollutants, and knowledge about the effects of HBCD and PE pollution on soil bacterial communities remains obscure. In this study, the effects of different HBCD and PE concentrations and combined HBCD and PE exposure on the diversity, composition, and function of agricultural soil bacterial communities over 4 months were systematically examined for the first time. Generally, soil bacterial communities were influenced in both the 1-month and 4-month scenarios through HBCD and PE separately as well as combined exposure. After 4 months of exposure, PE and combined exposure significantly affected soil bacterial alpha diversity, however, low concentration of HBCD showed no apparent influence. 1-month and 4-month HBCD, PE, and combined exposure significantly influenced bacterial beta diversity. Compared with 1 month of exposure, HBCD, PE, and combined exposure demonstrated remarkable influences on soil bacteria after 4 months of exposure, especially on Nitrospirae, Elusimicrobia, Rokubacteria at the phylum level, and on MND1, Ruminiclostridium, Lysobacter, Anaeromyxobacter, Alistipes, WCHB1 at the genus level. The bacterial function analysis indicated that amino acid metabolism, carbohydrate metabolism, and membrane transport were the three predominant enriched bacterial functions after 1-month and 4-month HBCD and PE exposure. This research provides a comprehensive grasp of the effects of HBCD and PE pollution on soil microbial communities, which could have a beneficial impact on future soil pollution control.

Heavy Metal Contamination Alters the Co-Decomposition of Leaves of the Invasive Tree Rhus typhina L. and the Native Tree Koelreuteria paniculata Laxm.

Invasive and native plants can coexist in the same habitat; however, the decomposition process may be altered by the mixing of invasive and native leaves. Heavy metal contamination may further alter the co-decomposition of both leaf types. This study evaluated the effects of two concentrations (35 mg·L-1 and 70 mg·L-1) and three types (Pb, Cu, and combined Pb + Cu) of heavy metal contamination on the co-decomposition of leaves of the invasive tree Rhus typhina L. and the native tree Koelreuteria paniculata Laxm, as well as the mixed effect intensity of the co-decomposition of the mixed leaves. A polyethylene litterbag experiment was performed over six months. The decomposition coefficient of the two trees, mixed effect intensity of the co-decomposition, soil pH and enzymatic activities, soil bacterial alpha diversity, and soil bacterial community structure were determined. A high concentration of Pb and combined Pb + Cu significantly reduced the decomposition rate of R. typhina leaves. A high concentration of Pb or Cu significantly reduced the decomposition rate of the mixed leaves. In general, R. typhina leaves decomposed faster than K. paniculata leaves did. There were synergistic effects observed for the co-decomposition of the mixed leaves treated with combined Pb + Cu, regardless of concentration, but there were antagonistic effects observed for the co-decomposition of the mixed leaves treated with either Pb or Cu, regardless of concentration. A high concentration of Pb or Cu may increase antagonistic effects regarding the co-decomposition of mixed-leaf groups. Thus, heavy metal contamination can significantly affect the intensity of the mixed effect on the co-decomposition of heterogeneous groups of leaves.

Changes in grassland soil types lead to different characteristics of bacterial and fungal communities in Northwest Liaoning, China.

Soil microbial communities are critical in regulating grassland biogeochemical cycles and ecosystem functions, but the mechanisms of how environmental factors affect changes in the structural composition and diversity of soil microbial communities in different grassland soil types is not fully understood in northwest Liaoning, China. We investigated the characteristics and drivers of bacterial and fungal communities in 4 grassland soil types with 11 sites across this region using high-throughput Illumina sequencing. Actinobacteria and Ascomycota were the dominant phyla of bacterial and fungal communities, respectively, but their relative abundances were not significantly different among different grassland soil types. The abundance, number of OTUs, number of species and diversity of both bacterial and fungal communities in warm and temperate ecotone soil were the highest, while the warm-temperate shrub soil had the lowest microbial diversity. Besides, environmental factors were not significantly correlated with soil bacterial Alpha diversity index. However, there was a highly significant negative correlation between soil pH and Shannon index of fungal communities, and a highly significant positive correlation between plant cover and Chao1 index as well as Observed species of fungal communities. Analysis of similarities showed that the structural composition of microbial communities differed significantly among different grassland soil types. Meanwhile, the microbial community structure of temperate steppe-sandy soil was significantly different from that of other grassland soil types. Redundancy analysis revealed that soil total nitrogen content, pH and conductivity were important influencing factors causing changes in soil bacterial communities, while soil organic carbon, total nitrogen content and conductivity mainly drove the differentiation of soil fungal communities. In addition, the degree of connection in the soil bacterial network of grassland was much higher than that in the fungal network and soil bacterial and fungal communities were inconsistently limited by environmental factors. Our results showed that the microbial community structure, composition and diversity of different grassland soil types in northwest Liaoning differed significantly and were significantly influenced by environmental factors. Microbial community structure and the observation of soil total nitrogen and organic carbon content can predict the health changes of grassland ecosystems to a certain extent.

Adaptations of Potential Nitrogenase Activity and Microbiota with Long-Term Application of Manure Compost to Paddy Soil

Biological nitrogen fixation complements nitrogen from fertilizers in crop plants under natural conditions. It also contributes to the reduction in chemical fertilizer (CF) utilization in cultivated lands, which fits the concept of sustainable agriculture. From this viewpoint, however, it is still unknown in paddy fields how soil bacterial nitrogenase and microbiota are affected by applied materials in the soil. Therefore, in this study, the effects of long-term material applications on potential nitrogenase activity and the microbiota of soil bacteria were investigated. The nitrogenase activity tended to be higher in manure compost (MC)-applied soils than in CF-applied soils in both summer and winter. Soil bacterial alpha diversity increased whereas soil ammonia availability decreased with the MC application. The dynamic response of soil bacterial microbiota was caused by the MC application. The abundance of Nitrospira, a class of ammonia and nitrite oxidation bacteria, was lower and the abundance of alpha-Proteobacteria was higher in the MC-applied soils than in the CF-applied soils. These results suggest that the alpha diversity increase and restricted availability of NH3-N might contribute to the increase in potential nitrogenase activity in the long-term MC-applied soils.

Potential effect of key soil bacterial taxa on the increase of rice yield under milk vetch rotation.

Legume crop rotation is often adopted in rice cultivation to improve soil productivity. However, little is known about the role of microbes under legume rotation in affecting soil productivity. To elucidate this, a long-term paddy cropping experiment was set up to study the relationship between crop yield, soil chemical properties, and key microbial taxa under a double-rice and milk vetch rotation. Milk vetch rotation significantly improved soil chemical properties compared to no fertilization treatment, and soil phosphorus was a major factor correlated with crop yield. Long-term legume rotation increased soil bacterial alpha diversity and changed soil bacterial community. After milk vetch rotation, the relative abundances of Bacteroidota, Desulfobacterota, Firmicutes, and Proteobacteria increased while those of Acidobacteriota, Chloroflexi, and Planctomycetota decreased. Moreover, milk vetch rotation increased the relative abundance of phosphorus-related gene K01083 (bpp), which was significantly correlated with soil phosphorus content and crop yield. Network analysis showed that taxa of Vicinamibacterales were positively correlated with total phosphorus and available phosphorus, which was a potential taxon contributing to the availability of soil phosphorus stock. Our results indicated that milk vetch rotation could enrich key taxa with latent phosphate-solubilizing ability, increase the content of soil available phosphorus, and finally enhance crop yield. This could provide scientific guidance for better crop production.

Impact of Cover Crops and Nitrogen Management on Soil Bacterial Alpha Diversity

ABSTRACT Corn (Zea mays L.) nitrogen (N) strategies that account for fertilizer timing and source may differentially affect soil bacterial communities and require further validation when preceded by cover crops (CC). Field studies were conducted (2014–2016) evaluating the effects of daikon radish [Raphanus sativus (L.)], forage oat [Avena sativa (L.)], and no CC combined with multiple N management strategies on soil bacterial alpha diversity metrics. Nitrogen strategies consisted of 179 kg N ha−1 applied pre-plant incorporated (PPI), poultry litter (PL) (61 kg N ha−1) applied PPI plus sidedress (SD) N at V11 (11 leaf collars), starter N (45 kg N ha−1) applied 5 cm beside and below the furrow followed by SD at V4 (4 leaf collars), V11, or 50:50 (split) V4 and V11, and a zero N control. In 1 of 2 years, radish reduced diversity 47–53% during active growth compared to remaining treatments. Inverse relationships regarding diversity of in-row (IR) soils at R1 (silking) and grain yield indicated that increased bacterial diversity did not correspond to increased grain production. Relative to PL and the zero-N control, starter N strategies reduced R1 rhizosphere bacterial diversity, evenness, and richness. Combining organic with soluble N sources may stabilize changes to soil alpha diversity metrics at corn silking.

Cultivation in an Alpine Region: Implications for Soil Bacteria

Land use change is a major predictor for variations in soil bacteria, which plays a key role in maintaining soil multifunctionality and function of terrestrial ecosystems. The effects of land use change on the soil bacterial community in an alpine region at the Qinghai-Tibetan Plateau (QTP) were still unclear. In this study, we investigated soil bacterial profiles under grazed grassland, enclosed grassland, continuous cropland, rotation cropland and abandoned cropland in the Tianzhu alpine agro-pastoral ecotone. Our results showed that Proteobacteria, Acidobacteria and Actinobacteria were the most three abundant phyla regardless of land use change, accounting for over 60% of the total. Cultivation declined soil bacterial alpha diversity without recovering even after abandonment. Over 73% variations in bacterial diversity can be explained by soil physical and chemical properties. In addition, soil moisture could be the main driver for the difference in bacterial structure between croplands and others. Soil bulk density, pH, organic carbon and total nitrogen contents seem to be the key factors determining the difference in bacterial structure between abandoned croplands and others. Our results have implications for comprehensive understanding about the responses of the soil bacterial community to land use change in alpine regions.

Soil bacterial communities and co-occurrence changes associated with multi-nutrient cycling under rice-wheat rotation reclamation in coastal wetland

Coastal reclamation is a global threat to coastal wetland ecosystems, but the impacts of coastal reclamation on belowground biodiversity and their consequences for ecosystem nutrient cycling remain poorly understood. In this study, we examined soil bacterial communities, bacterial co-occurrence pattern and soil multi-nutrient cycling index after natural vegetated coastal wetlands were converted for 6-year and 30-year rice-wheat rotation fields. The soil multi-nutrient cycling index was higher in 6-year and 30-year rice-wheat rotation fields than natural vegetated coastal wetlands. For bacterial community, rice-wheat rotation reclamation increased soil bacterial alpha diversity but decreased beta diversity and co-occurrence network complexity than those in the vegetated coastal wetland. Rice-wheat rotation reclamation also changed soil bacterial community assemblages by increasing the relative abundance of Actinobacteriota and Desulfobacterota while decreasing the relative abundance of Alphaproteobacteria and Gammproteobacteria. Changes in the relative importance of dispersal limitation and homogenizing dispersal mainly controlled the variations in soil bacterial community assemblages. Soil bacterial community variations induced by rice-wheat reclamation were strongly related to soil multi-nutrient cycling, especially bacterial connection complexity. Our results provide experimental support that belowground microbial interactions are crucial for maintaining ecosystem functioning.

Long-Term Wheat-Soybean Rotation and the Effect of Straw Retention on the Soil Nutrition Content and Bacterial Community

Straw retention and wheat-soybean rotation play critical role in maintaining soil quality. However, the correlation between bacterial diversity and community structure, and soil nutrients is unknown, and a systematic understanding of their responses to straw retention is lacking. In the field experiment, the straw retention treatments included no straw (NS), half straw (HS), and total straw (TS) retention during long-term wheat-soybean rotation. The mean contents of soil total nitrogen (TN), nitrate-N (NO3−-N), and microbial biomass nitrogen (MBN) increased by 15.06%, 21.10%, and 38.23%, respectively, with straw retention relative to NS, while that of ammonium-N (NH4+-N) reduced by 3.68%. The concentration of carbon components increased as straw retention increased. The levels of soil dissolved organic carbon (DOC), microbial biomass carbon (MBC), and soil organic carbon (SOC) increased by 4.34%, 7.63%, and 9.34%, respectively, with straw retention relative to NS. Soil bacterial alpha diversity was reduced with straw retention. Soil pH and nutrient content were identified as the main factors affecting the soil microbial diversity and structure at the phylum level. Accordingly, straw retention and soybean-wheat rotation enable sustainable agriculture in the dryland of northern China.

Forest gaps alter the soil bacterial community of weeping cypress plantations by modulating the understory plant diversity.

Weeping cypress is an endemic tree species that is widely planted in China, and the simple stand structure and fragile ecosystem of its plantation are common issues. Exploring the effect of different gap sizes on the soil bacterial community structure of weeping cypress plantations can provide a theoretical basis for the near-natural management of forest plantations. We, therefore, constructed three kinds of forest gaps with different sizes in weeping cypress plantations, namely, small (50–100 m2), medium (100–200 m2), and large gaps (400–667 m2), for identifying the key factors that affect soil bacterial communities following the construction of forest gaps. The results suggested that the herb layer was more sensitive than the shrub layer, while the Simpson, Shannon, and richness indices of the herb layer in plots with gaps were significantly higher than those of designated sampling plots without any gaps (CK). The presence of large gaps significantly increased the understory plant diversity and the Shannon and Simpson indices of the soil bacterial alpha diversity. There were obvious changes in the community composition of soil bacteria following the construction of forest gaps. The dominant bacterial phyla, orders, and functions were similar across the plots with different gap sizes. Of the indicator bacterial species, the abundance of the nitrogen-fixing bacteria, Lysobacter_ yangpyeongensis, and Ensifer_meliloti, was significantly different across plots with different gap sizes and accounted for a large proportion of the bacterial population of plots with medium and large gaps. The understory plant diversity was mostly related to the soil bacterial community than to other soil factors. The results of structural equation modeling indicated that the understory plant diversity was the most important environmental factor in driving the composition and diversity of bacterial communities. The construction of forest gaps significantly improved the understory plant diversity, physicochemical properties of the soil, and bacterial diversity in weeping cypress plantations, and the results of the comprehensive evaluation were in the order: large gaps > small gaps > medium gaps > CK. Our results suggested that large gaps are beneficial for the diversity of above-ground plant communities and underground soil bacterial communities.

Vegetation restoration increases the diversity of bacterial communities in deep soils

Soil microbial communities are engineers of key biogeochemical processes and mediate the functioning of vegetation restoration ecosystems following cropland abandonment. However, how microbial communities in the deep soil profile, especially the complexity and stability of their interactions, respond to vegetation restoration remains unclear. Here, we explored the soil properties and bacterial community diversity, structure, and network interactions and attempted to identify the keystone taxa along the 0–500 cm soil profile under different land use types (cropland, restored woodland, restored grassland). The results showed soil bacterial alpha diversity, indicated by phylotype richness and Shannon diversity index, was higher in deeper soil layers under restored lands (woodland and grassland) compared to long-term cultivated cropland. The dominant phyla of bacterial communities included Actinobacteria, Proteobacteria, Chloroflexi, Acidobacteria, and GAL15. Using the molecular ecological network approach, we confirmed bacterial ecological networks were more complex in restored woodland and grassland, compared to cropland, indicating the bacterial species have greater niche-sharing and more interactions over the whole 0–500 cm profile under restored ecosystems. Moreover, relatively large and intricate bacterial interactions persisted in the soil deep layer (380–400 cm). Soil available phosphorus (P), organic carbon, and total P contents, fine root length density, and soil moisture conditions strongly affected microbial communities after vegetation restoration. In general, our findings have implications for understanding the potential of restored ecosystems to withstand disturbances under global climate change scenarios.

Erosion-deposition positively reconstruct the bacterial community and negatively weaken the fungal community

Soil erosion and deposition are general ecological processes that have been widely described in terms of their effects on the physical and chemical properties of soil. However, their effects on soil microbes remain unclear, especially how microbial communities respond to erosion–deposition in soils with different organic carbon levels. A long-term field experiment was conducted to examine the effects of erosion and deposition on soil microbial communities across full slopes with different organic carbon levels on the Loess Plateau of China. The results showed that erosion reduced soil bacterial alpha diversity, weakened bacterial network complexity while deposition increased bacterial alpha diversity, and enhanced the complexity of the bacterial network. However, both erosion and deposition caused a decrease in fungal alpha diversity and network complexity. There was a weak reverse cooperative covariation relationship between bacterial and fungal alpha diversity. There was a higher bacterial and fungal diversity at the eroded and depositional sites with high soil organic carbon (SOC) level than low and medium SOC levels. An increase in the SOC level effectively strengthened the network complexity of bacteria and fungi at the eroded and depositional sites.. Erosion-deposition and SOC levels significantly increased variation in bacterial community structure. In contrast, the fungal community structure only differed at the eroded and depositional sites at high SOC levels. The key factors driving variation in bacterial community structure in soil properties were not significantly affected by SOC levels. Conversely, key factors resulting in differences in fungal community structure were regulated by the SOC level. Our results demonstrate that erosion–deposition reconstruct the bacterial community and weakens the fungal community, organic carbon regulate soil microbial communities and functions by controlling earth surface processes induced by erosion–deposition.

Diversity patterns and drivers of soil bacterial and fungal communities along elevational gradients in the Southern Himalayas, China

Elucidating the diversity patterns and drivers of soil microbes at high altitudes contributes to understanding the role microbes play in ecosystem services, but little is known about the soil microbial diversity, richness and abundance patterns across elevations on the Tibetan Plateau. This study was conducted to explore the shifts of forest soil bacterial and fungal community diversities and the regulating factors along an elevation gradient (2980–4050 m a.s.l.) in the Southern Himalayas of China. Illumina sequencing of 16S rRNA and ITS1, and quantitative real-time PCR were used to determine soil bacterial and fungal communities, coupled with plant diversity survey and edaphic properties analysis. The results revealed that plant alpha-diversity reached the highest level at an elevation of 3255 m and subsequently decreased with higher elevations; while soil bacterial alpha-diversity and fungal richness reached the lowest at 3590 m and 3772 m respectively, then increased with higher elevations; soil microbial abundance decreased with increasing elevation. The soil pH was the main driver of the elevation-related soil bacterial richness, diversity, and abundance. Soil nutrients contributed most to the fungal richness, diversity, and abundance. The total phosphorus content was the optimal predictor of fungal richness and abundance, while nitrate levels determined the fungal diversity. The community structures of bacteria and fungi differed significantly among elevations (Pbacteria = 0.001, Pfungi = 0.001). The elevation and edaphic properties (including the contents of soil organic matter and pH) controlled the elevation patterns of soil bacterial community structures and explained 56.1 % of the total variation. In contrast, edaphic properties (including SOC, TP and pH) primarily shaped the elevation patterns of soil fungal community structures and explained 38.7 % of the total variation. This study provides comprehensive insights into soil microbial geography associated with the biogeochemical cycling on the Tibetan Plateau.

Effects of Forest Gaps on the Structure and Diversity of Soil Bacterial Communities in Weeping Cypress Forest Plantations.

The decline in forest ecological function caused by pure forest plantations planted in the Yangtze River basin is becoming increasingly serious. To investigate this problem, we selected the local low-efficiency weeping cypress plantations for forest gap transformation. Three forest gap sizes, specifically large, medium, and small gaps, were established, and the effects of gap sizes on soil bacterial community structure and diversity in winter and summer were studied compared to no gaps (CK; control). Compared to CK, forest gaps had a significant effect on soil organic carbon (SOC) and soil total nitrogen (TN), and the highest values of SOC and soil TN under two seasons occurred in large forest gaps. The interactions of forest gap sizes and seasons had significant effects on pH, SOC, TN, and alpha diversity indices, including Simpson, Chao1, and ACE indices. Compared to winter, forest gaps significantly increased the soil bacterial community diversity indices in summer. Forest gap sizes significantly affected the composition of the bacterial community, but the composition of the dominant bacteria at the phyla and genera levels was similar. Linear discriminant effect size (LEfSe) analysis showed that there were 32 indicator bacterial species in two seasons. Co-occurrence network analysis revealed that the relationship of the soil bacterial community at the phyla level was complex, and there was a significant positive correlation among bacterial species. Soil bulk density (BD) and soil moisture (SM) significantly affected the soil bacterial alpha diversity indices. The composition of the dominant bacteria at the phyla level was significantly affected by soil microbial carbon (MBC), whereas the composition of dominant bacteria at the genera level was affected by soil hydrolysable nitrogen (AN) and the carbon/nitrogen (C/N) ratio. In this study, compared to the other forest gaps, large forest gaps were more conducive to the accumulation of soil nutrients, thus improving the structure of the soil bacterial community. Importantly, changes in the soil bacterial community structure due to gap formation may have profound effects on soil biogeochemical processes in weeping cypress forest plantations.

Difference of Bacterial Community Structure in the Meadow, Maize, and Continuous Cropped Alfalfa in Northeast China.

Maize and alfalfa (Medicago sativa L.) have been used extensively in the animal husbandry to compensate for the lack of livestock and fodder yields in the chilly northeast of China. Little is known, however, about the impact on soil characteristics of consecutive plantings in various crops and alfalfa. In this research, the soil characteristics, bacterial community diversity, and structure of the meadow, maize, and alfalfa continuous cropping fields (i.e., 6, 10, 14, 20, and 30 years) were measured. The results showed that maize cropping and continuous cropping of alfalfa increased the soil bacterial alpha diversity compared with meadow cropping, and alpha diversity of alfalfa increased with the continuous planting years. Soil pH, total phosphorus (TP), available P, total potassium (TK), and nitrate nitrogen (NO3–) content were soil variables significantly impacting the structure of soil bacterial communities in different plant types and different alfalfa continuous cropping systems. In addition, the relative abundance of some beneficial microbial species, such as Arthrobacter and Gaiellales, in the cropping maize and continuous cropping of alfalfa was much higher than that in the meadow field. Moreover, the networks differ among different plant types, and also differ among different continuous cropping years of alfalfa, and topologies of the networks suggested that continuous planting of alfalfa promotes cooperation between bacteria, which facilitates the long growth of alfalfa and is beneficial to the soil.

Effect of fertilizer management on the soil bacterial community in agroecosystems across the globe

Different types of fertilizer can significantly change soil fertility. The response of soil bacterial communities to different fertilization regimes has been studied widely, but the inconsistent results urged us to systematically study the effect of multiple environmental factors on bacterial diversity and composition under different fertilization regimes. Here, we conduct a meta-analysis of a global dataset from 105 publications to explore the effect of mineral nitrogen, straw, and manure addition on soil bacterial alpha-diversity (Shannon and Chao1 indices) and community composition. Mineral nitrogen and straw addition decreased the Shannon (mineral nitrogen: –4.48%; straw: –11.83%) and Chao1 (mineral nitrogen: –0.97%; straw: –11.57%) indices, while manure addition increased the Shannon (0.53%) and Chao1 (5.64%) indices. The three types of fertilizer all favored the growth of Proteobacteria, Actinobacteria, and Bacteroidetes and inhibited the growth of Acidobacteria and Nitrospirae. Manure addition had the greatest increase in the abundance of Proteobacteria, Bacteroidetes, and the least decrease in abundance of Nitrospirae. Manure addition increased soil organic carbon, total soil nitrogen, and soil microbial biomass carbon more than mineral nitrogen and straw addition. Mineral nitrogen and straw addition decreased soil pH, while manure addition increased soil pH. Soil environmental and climate factors significantly drove changes in bacterial alpha-diversity and community, particularly soil pH. In conclusion, manure addition is the preferred fertilization management for most agricultural ecosystems. These results can be used as a valuable reference for agricultural management strategies to maintain belowground bacterial diversity and composition in agroecosystems across the globe.

Rhizosphere Soil Bacterial Communities of Continuous Cropping-Tolerant and Sensitive Soybean Genotypes Respond Differently to Long-Term Continuous Cropping in Mollisols.

The continuous planting of soybeans leads to soil acidification, aggravation of soil-borne diseases, reduction in soil enzyme activity, and accumulation of toxins in the soil. Microorganisms in the rhizosphere play a very important role in maintaining the sustainability of the soil ecosystem and plant health. In this study, two soybean genotypes, one bred for continuous cropping and the other not, were grown in a Mollisol in northeast China under continuous cropping for 7 and 36years in comparison with soybean–maize rotation, and microbial communities in the rhizosphere composition were assessed using high-throughput sequencing technology. The results showed that short- or long-term continuous cropping had no significant effect on the rhizosphere soil bacterial alpha diversity. Short-term continuous planting increased the number of soybean cyst nematode (Heterodera glycines), while long-term continuous planting reduced these numbers. There were less soybean cyst nematodes in the rhizosphere of the tolerant genotypes than sensitive genotypes. In addition, continuous cropping significantly increased the potential beneficial bacterial populations, such as Pseudoxanthomonas, Nitrospira, and Streptomyces compared to rotation and short-term continuous cropping, suggesting that long-term continuous cropping of soybean shifts the microbial community toward a healthy crop rotation system. Soybean genotypes that are tolerant to soybean might recruit some microorganisms that enhance the resistance of soybeans to long-term continuous cropping. Moreover, the network of the two genotypes responded differently to continuous cropping. The tolerant genotype responded positively to continuous cropping, while for the sensitive genotype, topology analyses on the instability of microbial community in the rhizosphere suggested that short periods of continuous planting can have a detrimental effect on microbial community stability, although this effect could be alleviated with increasing periods of continuous planting.