[Intensive Citrus Cultivation Suppresses Soil Phosphorus Cycling Microbial Activity].

Soil microbes are key drivers in regulating the phosphorus cycle. Elucidating the microbial mineralization process of soil phosphorus-solubilizing bacteria is of great significance for improving nutrient uptake and yield of crops. This study investigated the mechanism by which citrus cultivation affects the soil microbial acquisition strategy for phosphorus by measuring the abundance of the phoD gene, microbial community diversity and structure, and soil phosphorus fractions in the soils of citrus orchards and adjacent natural forests. The results showed that citrus cultivation could lead to a decrease in soil pH and an accumulation of available phosphorus in the soil, with a content as high as 112 mg·kg-1, which was significantly higher than that of natural forests (3.7 mg·kg-1). Citrus cultivation also affected the soil phosphorus fractions, with citrus soil having higher levels of soluble phosphorus (CaCl2-P), citrate-extractable phosphorus (Citrate-P), and mineral-bound phosphorus (HCl-P). The phosphorus fractions of natural forest soils were significantly lower than those of citrus soils, whereas the phoD gene abundance and alkaline phosphatase activity were significantly higher in natural forest soils than in citrus soils. High-throughput sequencing results showed that the Shannon diversity index of phosphate-solubilizing bacteria in citrus soils was 4.61, which was significantly lower than that of natural forests (5.35). The microbial community structure in natural forests was also different from that of citrus soils. In addition, the microbial community composition of phosphate-solubilizing bacteria in citrus soils was also different from that of natural forests, with the relative abundance of Proteobacteria being lower in natural forest soils than in citrus soils. Therefore, citrus cultivation led to a shift of soil microbial acquisition strategy for phosphorus, with external phosphorus addition being the main strategy in citrus soils, whereas microbial mineralization of organic phosphorus was the main strategy in natural forest soils to meet their growth requirements.

Sediment depth-related variations of comammox Nitrospira: Evidence in the Three Gorges Reservoir, China.

The recent discovery of comammox Nitrospira as complete ammonia-oxidizing microorganism has fundamentally revolutionized our understanding of nitrogen cycling in sediment environments. However, knowledge regarding their abundance, biodiversity, community structure, and interactions is predominantly limited to the upper layers (0-20 cm). To address this gap, we collected sediment samples along profiles ranging from 0 to 300 cm in depth at three locations within the middle segment of the Three Gorges Reservoir (TGR), China. Quantitative real-time PCR (qPCR) analyses suggested that comammox bacteria were not only ubiquitous in deep sediments but also more abundant than ammonia-oxidizing bacteria (AOB). Ammonia monooxygenases subunit A (amoA) gene amplicon sequencing illuminated that comammox bacteria were more sensitive to sedimental depth compared to AOB and ammonia-oxidizing archaea (AOA), as evidenced by a more significant decline in community diversity and similarity over distance along sediment vertical profiles. Notably, we discovered that the amoA gene abundance, alpha- and beta-diversity of comammox bacteria exerted an essential contribution to potential nitrification rates according to random forest model. Phylogenetic analysis indicted that most comammox bacteria within sediment samples belonged to clade A.2. Intriguingly, the average relative abundance of comammox clade A.2 displayed a noteworthy rise with sediment depth, whereas clade A.1 demonstrated a converse pattern, unveiling distinct ecological niche adaptations of these two clades along the sediment profile. Ecological network analysis further revealed closer interactions between comammox bacteria and canonical ammonia oxidizers in the superficial layer (0-40 cm), with the network structure gradually simplifying from superficial to deep sediment (200-300 cm). Overall, these findings broaden the current recognition of the geographic distribution and niche segregation of comammox bacteria at the fine scale of the sediments ecosystems and provide insights into sediment depth-related variations of their coexistence network patterns in large freshwater reservoirs.

Vertical variation in prokaryotic community composition and co-occurrence patterns in sediments of the Three Gorges Reservoir, China.

Archaea and bacteria are distributed throughout the sediment; however, our understanding of their biodiversity patterns, community composition, and interactions is primarily limited to the surface horizons (0-20 cm). In this research, sediment samples were collected from three vertical sediment profiles (depths of 0-295 cm) in the Three Gorges Reservoir (TGR), one of the largest reservoirs in the world. Through 16S rRNA sequencing, it was shown that sediment microbial diversity did not significantly vary across the sediment. Nevertheless, a decline in the similarity of archaeal and bacterial communities over distance along sediment vertical profiles was noted. Nonmetric multidimensional scaling (NMDS) analysis revealed that archaeal and bacterial communities could be clearly separated into two groups, located in the upper sediments (0-135 cm) and deep sediments (155-295 cm). Meanwhile, at the fine-scale of the vertical section, noteworthy variations were observed in the relative abundance of prominent archaea (e.g., Euryarchaeota) and bacteria (e.g., Proteobacteria). The linear discriminant analysis effect size (LEfSe) demonstrated that twenty-four bacterial and twenty-six archaeal biomarker microbes exist in the upper and deep sediment layers. Each layer exhibited distinctive microbial divisions, suggesting that microbes with diverse biological functions are capable of thriving and propagating along the sediment profile. Co-occurrence network analysis further indicated that the microbial network in the upper sediments was more complex than that in the deep sediments. Additionally, the newly discovered anaerobic methanotrophic archaeon Candidatus Methanoperedens was identified as the most abundant keystone archaeal taxon in both sediment layers, highlighting the significance of methane oxidation in material cycling within the TGR ecosystem. In summary, our study examined the biodiversity and coexistence patterns of benthic microbial communities throughout the vertical sediment profile, providing detailed insights into the vertical geography of archaeal and bacterial communities in typical deep-water reservoir ecosystems.

Biogeographic distribution of autotrophic bacteria was more affected by precipitation than by soil properties in an arid area.

Introduction: Autotrophic bacteria play an important role in carbon dioxide fixation and are widespread in terrestrial ecosystems. However, the biogeographic patterns of autotrophic bacteria and the driving factors still remain poorly understood. Methods: Herein, we conducted a 391-km north to south transect (mean annual precipitation <600 mm) survey in the Loess Plateau of China, to investigate the biogeographic distributions of autotrophic bacteria (RubisCO cbbL and cbbM genes) and the environmental drivers across different latitude sites with clear vegetational and climatic gradients. Results and discussion: The soils in northern region with lower precipitation are dominated by grassland/forest, which is typically separated from the soils in southern region with higher precipitation. The community structure of autotrophic bacterial cbbL and cbbM genes generally differed between the soils in the southern and northern Loess Plateau, suggesting that precipitation and its related land use practices/ecosystem types, rather than local soil properties, are more important in shaping the soil autotrophic microorganisms. The cbbL-containing generalist OTUs were almost equally abundant across the northern and southern Loess Plateau, while the cbbM-containing bacterial taxa were more prevalent in the low precipitation northern region. Such differences indicate differentiate distribution patterns of cbbM- and cbbL-containing bacteria across the north to south transect. Our results suggest that the community composition and the differentiate distributions of soil cbbL- and cbbM-containing bacterial communities depend on precipitation and the related ecosystem types in the north to south transect in the Loess Plateau of China.

Disentangling drivers of soil microbial nutrient limitation in intensive agricultural and natural ecosystems.

Characterized by continuous chemical fertilization, intensive agriculture generally reduces soil ecoenzymatic activities and nutrient mineralization, as well as alters the biomass production and microbial community composition. Soil acidification poses serious threats to the sustainable development of intensive agriculture. However, the mechanism of nutrient cycling and metabolism of soil microorganisms in response to soil acidification in intensive agriculture remains unclear. Herein, we studied the variations in ecoenzymatic stoichiometry of soil ß-glucosidase (BG), cellobiohydrolase (CBH), N-acetylglucosaminidase (NAG) and acid phosphatase (AP) under different land use types and pH gradients of tea garden soils. The results revealed that natural forest and cropland soils had significantly higher BG and CBH activities than tea garden soils. Soil BG and CBH activities displayed significant positive correlations with soil pH, total nitrogen (TN) and phosphorus (TP), while soil NAG activity was significantly associated with nitrate nitrogen, total carbon (TC), TN, carbon: phosphorus (C:P) and nitrogen: phosphorus (N:P) ratios. Soil AP activity showed significant negative associations with pH, TP and C:N ratio, but was significantly positively correlated with TC, TN, C:P and N:P ratios. Enzyme vector model revealed that soil microorganisms are limited by P (enzyme vector angle >45°) regardless of land use types. Compared to natural forest soils, the P limitation of microorganisms in tea garden soils became increasingly serious with a decreasing pH gradient, as indicated by the significant increase in enzyme vector angle. Thus, the overall ecoenzymatic stoichiometry was shifted by soil pH. In summary, higher pH increased BG activity and decreased AP activity, but had no significant effect on NAG activity, suggesting co-limitation of soil microorganisms by C and P in this area. This study provides novel insights into the effect of soil acidification on ecoenzymatic stoichiometry, and also highlights the stoichiometric and energy limitations on the metabolism of soil microorganisms in agricultural ecosystems.

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

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.

Biogeography and the driving factors affecting forest soil bacteria in an arid area.

Bacteria are one of the most abundant and diverse groups and mediate many critical terrestrial ecosystem processes. Despite the crucial ecological role of bacteria, our understanding of their large-scale biogeography patterns across longitude (east-west transect), and the processes that determine these patterns lags significantly behind that of macro-organisms. Here, we used 16S rRNA gene sequencing to evaluate the geographic distributions of bacterial diversity and their driving factors across different longitude sites along an 800-km east-west transect in the Loess Plateau. Twenty-four phyla were detected across all soil samples and the most sequence-abundant bacterial phyla were Acidobacteria, Actinobacteria, Alphaproteobacteria, Betaproteobacteria, Chloroflexi and Gemmatimonadetes (average relative abundance >5%). Soil bacterial α-diversity, expressed by the richness of soil bacterial communities and Shannon diversity, differed among climates (MAP) but showed strong correlations with MAP (r=-0.537 and r=-0.42, respectively; p<0.05 in both bacterial diversity indices). Variation partition analysis demonstrated that the bacterial community structure was closely correlated with environmental variables and geographic distance, which together explained 62% of the community variation. Soil properties contributed more to bacterial community variation than the combined geographic distance (historical contingencies) and climate factors. Among all environmental factors, soil pH exhibited a dominant role in structuring bacterial communities in this arid area. Our findings provide new evidence of bacterial biogeography patterns in an arid area (MAP ranged from 473mm to 547mm). Additionally, the results indicated a close linkage among soil bacterial community, climate and edaphic variables, which is critical for predicting promoting sustainable ecosystem services in the Loess Plateau.

[Effects of the Farmland-to-Forest/Grassland Conversion Program on the Soil Bacterial Community in the Loess Hilly Region].

This study investigated the effects of the program aimed at converting farmland into forest or grassland on the soil bacterial diversity in the Loess Hilly region. Corn land was selected as the experimental control, and Caragana intermedia land and Stipa bungeana land were selected as the experimental lands. Soil from three different land use types were selected as subjects. The soil bacterial communities were analyzed using a high throughput sequencing technique (MiSeq). The sequence region was 16S rRNA V3-V4 variable region. The α diversity, community composition, and relative abundances of the soil bacterial groups were analyzed, in order to explore the effects of soil physical and chemical properties on the bacterial community structure. The results showed that the structure and diversity of the microbial communities differed under the different land use types. At the phylum level, the dominant phyla were Proteobacteria, Actinobacteria, Acidobacteria, Chloroflexi, Gemmatimonadetes, and Firmicutes. At the class level, α-Proteobacteria, Actinobacteria, Acidobacteria, ß-Proteobacteria, Thermoleophilia, Gemmatimonadetes, Bacilli, and δ-Proteobacteria were predominant. Compared to the corn land, Proteobacteria and Actinobacteria were the dominant bacteria in the Caragana intermedia land, while Actinobacteria and Acidobacteria were the dominant bacteria in the Stipa bungeana land. Soil bacterial diversity was the highest in the shrub land. RDA analysis revealed that soil organic matters and total nitrogen were the most influential environmental factors. It was shown thus that the program of converting farmland into forest or grassland has significantly improved the soil fertility and environmental conditions, and the composition of the soil bacterial community has also been appreciably changed.

Impact of litter quantity on the soil bacteria community during the decomposition of Quercus wutaishanica litter.

The forest ecosystem is the main component of terrestrial ecosystems. The global climate and the functions and processes of soil microbes in the ecosystem are all influenced by litter decomposition. The effects of litter decomposition on the abundance of soil microorganisms remain unknown. Here, we analyzed soil bacterial communities during the litter decomposition process in an incubation experiment under treatment with different litter quantities based on annual litterfall data (normal quantity, 200 g/(m2/yr); double quantity, 400 g/(m2/yr) and control, no litter). The results showed that litter quantity had significant effects on soil carbon fractions, nitrogen fractions, and bacterial community compositions, but significant differences were not found in the soil bacterial diversity. The normal litter quantity enhanced the relative abundance of Actinobacteria and Firmicutes and reduced the relative abundance of Bacteroidetes, Plantctomycets and Nitrospiare. The Beta-, Gamma-, and Deltaproteobacteria were significantly less abundant in the normal quantity litter addition treatment, and were subsequently more abundant in the double quantity litter addition treatment. The bacterial communities transitioned from Proteobacteria-dominant (Beta-, Gamma-, and Delta) to Actinobacteria-dominant during the decomposition of the normal quantity of litter. A cluster analysis showed that the double litter treatment and the control had similar bacterial community compositions. These results suggested that the double quantity litter limited the shift of the soil bacterial community. Our results indicate that litter decomposition alters bacterial dynamics under the accumulation of litter during the vegetation restoration process, which provides important significant guidelines for the management of forest ecosystems.

How Fencing Affects the Soil Quality and Plant Biomass in the Grassland of the Loess Plateau.

Overgrazing is a severe problem in several regions in Northwestern China and has caused serious land degradation. Secondary natural succession plays an important role in the accumulation of soil carbon and nitrogen contents. Estimating the effects of grazing exclusion on soil quality and plant diversity will improve our understanding of the succession process after overgrazing and promote judicious management of degraded pastures. This experiment was designed to measure soil properties and plant diversity following an age chronosequence of grasslands (ages ranged from one year, 12 years, 20 years, and 30 years) in Northwestern China. The results showed that continuous fencing resulted in a considerable increase in plant coverage, plant biomass (above- and below-ground biomass), and plant diversity, which can directly or indirectly improve the accumulation of soil organic carbon and total nitrogen content. The plant coverage and the above- and below-ground biomass linearly increased along the succession time, whereas soil organic C and N contents showed a significant decline in the first 12 years and, subsequently, a significant increase. The increased plant biomass caused an increase in soil organic carbon and soil total nitrogen. These results suggested that soil restoration and plant cover were an incongruous process. Generally, soil restoration is a slow process and falls behind vegetation recovery after grazing exclusion. Although the accumulation of soil C and N stocks needed a long term, vegetation restoration was a considerable option for the degraded grassland due to the significant increase of plant biomass, diversity, and soil C and N stocks. Therefore, fencing with natural succession should be considered in the design of future degraded pastures.

Soil bacterial community response to vegetation succession after fencing in the grassland of China.

Natural succession is an important process in terrestrial system, playing an important role in enhancing soil quality and plant diversity. Soil bacteria is the linkage between soil and plant, has an important role in aboveground community dynamics and ecosystem functioning in terrestrial ecosystems, driving the decomposition of soil organic matter and plant litter. However, the role of soil bacteria in the secondary succession has not been well understood, particularly in the degraded soil of Loess Plateau. In this study, we investigated soil nutrients and soil bacterial community during the secondary succession after a long-term fencing in the grassland, in the Yuwu Mountain, northwest China. The chronosequence included 1year, 12years, 20years and 30years. The soil bacterial community composition was determined by the Illumina HiSeq sequencing method. The data showed that soil bacterial diversity had no significant changes along the chronosequence, but soil bacterial community compositions significantly changed. Proteobacteria, Acidobacteria and Actinobacteria were the main phyla in all the samples across succession. With the accumulation of soil organic matter and nutrients, the relative abundance of Actinobacteria decreased, whereas Proteobacteria increased. These shifts may be caused by the increase of the available nutrients across the secondary succession. In the younger sites, soils were dominated by oligotrophic groups, whereas soil in the late-succession site were dominated by copiotrophic groups, indicating the dependence of soil bacterial community composition on the contents of soil available nutrients.

Soil, Leaf and Root Ecological Stoichiometry of Caragana korshinskii on the Loess Plateau of China in Relation to Plantation Age.

Caragana korshinskii, a leguminous shrub, a common specie, is widely planted to prevent soil erosion on the Loess Plateau. The objective of this study was to determine how the plantation ages affected soil, leaf and root nutrients and ecological stoichiometry. The chronosequence ages of C. korshinskii plantations selected for this study were 10, 20 and 30 years. Soil organic carbon (SOC) and soil total nitrogen (STN) of C. korshinskii plantations significantly increased with increase in the chronosequence age. However, soil total phosphorous (STP) was not affected by the chronosequence age. The soil C: N ratio decreased and the soil C: P and N: P ratios increased with increasing plantation age. The leaf and root concentrations of C, N, and P increased and the ratios C: N, C: P, and N: P decreased with age increase. Leaf N: P ratios were >20, indicating that P was the main factor limiting the growth of C. korshinskii. This study also demonstrated that the regeneration of natural grassland (NG) effectively preserved and enhanced soil nutrient contents. Compared with NG, shrub lands (C. korshinskii) had much lower soil nutrient concentrations, especially for long (>20 years) chronosequence age. Thus, the regeneration of natural grassland is an ecologically beneficial practice for the recovery of degraded soils in this area.

Bacterial Community Responses to Soils along a Latitudinal and Vegetation Gradient on the Loess Plateau, China.

Soil bacterial communities play an important role in nutrient recycling and storage in terrestrial ecosystems. Loess soils are one of the most important soil resources for maintaining the stability of vegetation ecosystems and are mainly distributed in northwest China. Estimating the distributions and affecting factors of soil bacterial communities associated with various types of vegetation will inform our understanding of the effect of vegetation restoration and climate change on these processes. In this study, we collected soil samples from 15 sites from north to south on the Loess Plateau of China that represent different ecosystem types and analyzed the distributions of soil bacterial communities by high-throughput 454 pyrosequencing. The results showed that the 142444 sequences were grouped into 36816 operational taxonomic units (OTUs) based on 97% similarity. The results of the analysis showed that the dominant taxonomic phyla observed in all samples were Actinobacteria, Proteobacteria, Chloroflexi, Acidobacteria and Planctomycetes. Actinobacteria and Proteobacteria were the two most abundant groups in all samples. The relative abundance of Actinobacteria increased from 14.73% to 40.22% as the ecosystem changed from forest to sandy, while the relative abundance of Proteobacteria decreased from 35.35% to 21.40%. Actinobacteria and Proteobacteria had significant correlations with mean annual precipitation (MAP), pH, and soil moisture and nutrients. MAP was significantly correlated with soil chemical and physical properties. The relative abundance of Actinobacteria, Proteobacteria and Planctomycetes correlated significantly with MAP, suggesting that MAP was a key factor that affected the soil bacterial community composition. However, along with the MAP gradient, Chloroflexi, Bacteroidetes and Cyanobacteria had narrow ranges that did not significantly vary with the soil and environmental factors. Overall, we conclude that the edaphic properties and/or vegetation types are driving bacterial community composition. MAP was a key factor that affects the composition of the soil bacteria on the Loess Plateau of China.

[Soil Bacterial Communities Under Different Vegetation Types in the Loess Plateau].

In this study, we collected soil samples from four different arborcommunities and four herb communities, which represented two vegetation ecosystems in the northwest of the Loess Plateau. Our objectives were to determine the diversity of soil bacterial communities and the affecting factors with the method of 454 high-throughput pyrosequencing technology. The results showed that the structures of the microbial communities differed in terms of both the predominant phylum and the relative abundance of each phylum. At the phylum level, the dominant phyla were Proteobacteria, Actinobacteria, Acidobacteria, Chloroflexi and Planctomycetes. At the class level, Actinobacteria, α-Proteobacteria, Acidobacteria, ß-Proteobacteria and Planctomycetacia were predominant. The relative abundance of Actinobacteria in grass vegetation ecosystem was more abundant than that in forest vegetation ecosystem. Proteobacteria in forest vegetation ecosystem were more abundant. Soil pH was significantly correlated with the relative abundance of Actinobacteria. Soil organic matter,soil total N and soil total P were the key factors affecting soil Proteobacteria. These results will provide useful information for the diversity of soil bacteria and guide the practice of vegetation restoration in the Loess Plateau.

[Characteristics of soil organic carbon and enzyme activities in soil aggregates under different vegetation zones on the Loess Plateau].

In order to explore the distribution characteristics of organic carbon of different forms and the active enzymes in soil aggregates with different particle sizes, soil samples were chosen from forest zone, forest-grass zone and grass zone in the Yanhe watershed of Loess Plateau to study the content of organic carbon, easily oxidized carbon, and humus carbon, and the activities of cellulase, ß-D-glucosidase, sucrose, urease and peroxidase, as well as the relations between the soil aggregates carbon and its components with the active soil enzymes were also analyzed. It was showed that the content of organic carbon and its components were in order of forest zone > grass zone > forest-grass zone, and the contents of three forms of organic carbon were the highest in the diameter group of 0.25-2 mm. The content of organic carbon and its components, as well as the activities of soil enzymes were higher in the soil layer of 0-10 cm than those in the 10-20 cm soil layer of different vegetation zones. The activities of cellulase, ß-D-glucosidase, sucrose and urease were in order of forest zone > grass zone > forest-grass zone. The peroxidase activity was in order of forest zone > forest-grass zone > grass zone. The activities of various soil enzymes increased with the decreasing soil particle diameter in the three vegetation zones. The activities of cellulose, peroxidase, sucrose and urease had significant positive correlations with the contents of various forms of organic carbon in the soil aggregates.