Effect of reclamation of abandoned salinized farmland on soil bacterial communities in arid northwest China

Land Use Types Drive the Distinct Patterns of Bacterial and Fungal Communities in Soils from the Semi-arid Area

Land types and ways of utilization significantly influence soil microbial communities in arid and semi-arid regions, which are vital for nutrient cycling and ecosystem functionality. In this study, the soil bacterial and fungal communities of five land types, including natural grasslands, farmlands, artificial grasslands, uncultivated lands, and riverbeds in the semi-arid lower reaches of the Heihe River, China, were investigated. Farmlands exhibited the highest bacterial Chao1 richness and Shannon diversity, while uncultivated soils had the lowest bacterial Chao1 richness. Fungal diversity was highest in uncultivated soils compared to farmlands. Principal coordinate analysis (PCoA) showed distinct microbial community structures across land types, with Actinobacteria, Proteobacteria, Firmicutes, and Chloroflexi dominating bacterial communities, and Ascomycota and Basidiomycota dominating fungal communities. Life history strategies revealed distinct patterns between bacterial and fungal communities within farmland soils and artificial grassland soils. Microbial community assembly in natural grasslands was primarily deterministic, with limited stochastic influence, while farmlands exhibited mixed assembly processes. Co-occurrence network analysis showed more stable and cooperative microbial networks in natural grasslands, while farmland networks were more competitive and reliant on key species. These findings provide important insights into the role of land use in shaping microbial diversity and ecosystem function, offering guidance for sustainable land management in semi-arid oasis regions.

Mangrove afforestation as an ecological control of invasive Spartina alterniflora affects rhizosphere soil physicochemical properties and bacterial community in a subtropical tidal estuarine wetland

Background

The planting of mangroves is extensively used to control the invasive plant Spartina alterniflora in coastal wetlands. Different plant species release diverse sets of small organic compounds that affect rhizosphere conditions and support high levels of microbial activity. The root-associated microbial community is crucial for plant health and soil nutrient cycling, and for maintaining the stability of the wetland ecosystem.

Methods

High-throughput sequencing was used to assess the structure and function of the soil bacterial communities in mudflat soil and in the rhizosphere soils of S. alterniflora, mangroves, and native plants in the Oujiang estuarine wetland, China. A distance-based redundancy analysis (based on Bray-Curtis metrics) was used to identify key soil factors driving bacterial community structure.

Results

S. alterniflora invasion and subsequent mangrove afforestation led to the formation of distinct bacterial communities. The main soil factors driving the structure of bacterial communities were electrical conductivity (EC), available potassium (AK), available phosphorus (AP), and organic matter (OM). S. alterniflora obviously increased EC, OM, available nitrogen (AN), and NO3 --N contents, and consequently attracted copiotrophic Bacteroidates to conduct invasion in the coastal areas. Mangroves, especially Kandelia obovata, were suitable pioneer species for restoration and recruited beneficial Desulfobacterota and Bacilli to the rhizosphere. These conditions ultimately increased the contents of AP, available sulfur (AS), and AN in soil. The native plant species Carex scabrifolia and Suaeda glauca affected coastal saline soil primarily by decreasing the EC, rather than by increasing nutrient contents. The predicted functions of bacterial communities in rhizosphere soils were related to active catabolism, whereas those of the bacterial community in mudflat soil were related to synthesis and resistance to environmental factors.

Conclusions

Ecological restoration using K. obovata has effectively improved a degraded coastal wetland mainly through increasing phosphorus availability and promoting the succession of the microbial community.

Effects of Nitrogen Forms on Soil Enzyme Activities in a Saline-Alkaline Grassland

Global climate change and agricultural practices have increased atmospheric nitrogen (N) deposition, significantly affecting the nitrogen cycling process in grasslands. The impact of different N forms on key soil enzyme activities involved in N nitrification, particularly in the saline-alkali grasslands of the Hexi Corridor, using natural grassland as a control (CK) and adding three N treatments: inorganic N (IN), organic N (ON) and a mixed N treatment (MN, with a 4:6 ratio of organic to inorganic N). Our study assessed the effects of these N forms on soil properties and enzyme activities crucial for N cycling. The findings indicate that different N forms significantly enhance soil mineral N content, with ON treatment leading to the highest increases in nitrate and ammonium content 92.44% and 35.6%, respectively, compared to CK. Both IN and ON treatments significantly boosted soil nitrate reductase and urease activities (p < 0.05), while MN treatment decreased nitrate reductase activity, with ON treatment showing the greatest sensitivity to enzyme activity changes. Soil pH slightly increased with N addition, but soil nitrite reductase activity remained relatively unchanged (0.372-0.385 mg g-1). Correlation analysis revealed that soil mineral N content and pH are key regulators of enzyme activities in saline-alkaline grasslands. These results suggest that different N forms should be considered in nutrient cycling models, with organic N addition potentially enhancing soil N conversion and mitigating nutrient limitations in grassland ecosystems.

High-throughput 16S rRNA gene-based amplicon sequencing reveals the functional divergence of halophilic bacterial communities in the Suaeda salsa root compartments on the eastern coast of China

The rhizosphere environment of plants, which harbors halophilic bacterial communities, faces significant challenges in coping with environmental stressors, particularly saline soil properties. This study utilizes a high-throughput 16S rRNA gene-based amplicon sequencing to investigate the variations in bacterial community dynamics in rhizosphere soil (RH), root surface soil (RS), root endophytic bacteria (PE) compartments of Suaeda salsa roots, and adjoining soils (CK) across six locations along the eastern coast of China: Nantong (NT), Yancheng (YC), Dalian (DL), Tianjin (TJ), Dongying (DY), and Qingdao (QD), all characterized by chloride-type saline soil. Variations in the physicochemical properties of the RH compartment were also evaluated. The results revealed significant changes in pH, electrical conductivity, total salt content, and ion concentrations in RH samples from different locations. Notably, the NT location exhibited the highest alkalinity and nitrogen availability. The pH variations were linked to HCO3- accumulation in S. salsa roots, while salinity stress influenced soil pH through H+ discharge. Despite salinity stress, enzymatic activities such as catalase and urease were higher in soils from various locations. The diversity and richness of bacterial communities were higher in specific locations, with Proteobacteria dominating PE samples from the DL location. Additionally, Vibrio and Marinobacter were prevalent in RH samples. Significant correlations were found between soil pH, salinity, nutrient content, and the abundance and diversity of bacterial taxa in RH samples. Bioinformatics analysis revealed the prevalence of halophilic bacteria, such as Bacillus, Halomonas, and Streptomyces, with diverse metabolic functions, including amino acid and carbohydrate metabolisms. Essential genes, such as auxin response factor (ARF) and GTPase-encoding genes, were abundant in RH samples, suggesting adaptive strategies for harsh environments. Likewise, proline/betaine transport protein genes were enriched, indicating potential bioremediation mechanisms against high salt stress. These findings provide insight into the metabolic adaptations facilitating resilience in saline ecosystems and contribute to understanding the complex interplay between soil conditions, bacterial communities, and plant adaptation.

Novel Bacillus and Prestia isolates from Dwarf century plant enhance crop yield and salinity tolerance

Soil salinity is a major environmental stressor impacting global food production. Staple crops like wheat experience significant yield losses in saline environments. Bioprospecting for beneficial microbes associated with stress-resistant plants offers a promising strategy for sustainable agriculture. We isolated two novel endophytic bacteria, Bacillus cereus (ADJ1) and Priestia aryabhattai (ADJ6), from Agave desmettiana Jacobi. Both strains displayed potent plant growth-promoting (PGP) traits, such as producing high amounts of indole-3-acetic acid (9.46, 10.00 µgml-1), ammonia (64.67, 108.97 µmol ml-1), zinc solubilization (Index of 3.33, 4.22, respectively), ACC deaminase production and biofilm formation. ADJ6 additionally showed inorganic phosphate solubilization (PSI of 2.77), atmospheric nitrogen fixation, and hydrogen cyanide production. Wheat seeds primed with these endophytes exhibited enhanced germination, improved growth profiles, and significantly increased yields in field trials. Notably, both ADJ1 and ADJ6 tolerated high salinity (up to 1.03 M) and significantly improved wheat germination and seedling growth under saline stress, acting both independently and synergistically. This study reveals promising stress-tolerance traits within endophytic bacteria from A. desmettiana. Exploiting such under-explored plant microbiomes offers a sustainable approach to developing salt-tolerant crops, mitigating the impact of climate change-induced salinization on global food security.

Microbiological impact of long-term wine grape cultivation on soil organic carbon in desert ecosystems: a study on rhizosphere and bulk sandy soils

The improvement of nutrients in soil is essential for using deserts and decertified ecosystems and promoting sustainable agriculture. Grapevines are suitable crops for desert soils as they can adapt to harsh environments and effectively impact soil nutrients; however, the mechanisms underlying this remain unclear. This study explored the impact of the different duration(3, 6, and 10 years) of grape cultivation on soil organic carbon, physicochemical properties, enzyme activities, microbial communities, and carbon cycle pathways in both rhizosphere and bulk soils. Partial least squares path modeling was used to further reveal how these factors contributed to soil nutrient improvement. Our findings indicate that after long-term grape cultivation six years, soil organic carbon, total nitrogen, total phosphorus, microbial biomass carbon and nitrogen, and enzyme activities has significantly increased in both rhizosphere and bulk soils but microbial diversity decreased in bulk soil. According to the microbial community assembly analysis, we found that stochastic processes, particularly homogenizing dispersal, were dominant in both soils. Bacteria are more sensitive to environmental changes than fungi. In the bulk soil, long-term grape cultivation leads to a reduction in ecological niches and an increase in salinity, resulting in a decrease in soil microbial diversity. Soil enzymes play an important role in increasing soil organic matter in bulk soil by decomposing plant litters, while fungi play an important role in increasing soil organic matter in the rhizosphere, possibly by decomposing fine roots and producing mycelia. Our findings enhance understanding of the mechanisms of soil organic carbon improvement under long-term grape cultivation and suggest that grapes are suitable crops for restoring desert ecosystems.

Composition and assembly mechanisms of prokaryotic communities in wetlands, and their relationships with different vegetation and reclamation methods

Coastal wetlands are undergoing substantial transformations globally as a result of increased human activities. However, compared to other ecosystems, diversity and functional characteristics of microbial communities in reclaimed coastal wetlands are not well studied compared to other ecosystems. This is important because it is known that microorganisms can play a crucial role in biogeochemical cycling within coastal wetland ecosystems. Hence, this study utilized the high-throughput sequencing technique to investigate the structure and assembly processes of microbial communities in reclaimed coastal wetlands. The results revealed a substantial change in soil properties following coastal wetland reclamation. Remarkably, the reclaimed soil exhibited significantly lower pH, soil organic carbon (SOC), and total salinity (TS) values (p < 0.05). The dominant phyla included Proteobacteria, Chloroflexi, Bacteroidetes, Acidobacteria, and Planctomycetes among study sites. However, the relative abundance of Proteobacteria increased from un-reclaimed coastal wetlands to reclaimed ones. The Proteobacteria, Chloroflexi, and Acidobacteria showed higher relative abundance in vegetated soil compared to bare soil, while Bacteroidetes and Planctomycetes exhibited the opposite trend. Notably, vegetation types exerted the strongest influence on microbial diversity, surpassing the effects of soil types and depth (F = 34.49, p < 0.001; F = 25.49, p < 0.001; F = 3.173, p < 0.078, respectively). Stochastic assembly processes dominated in un-reclaimed soil, whereas deterministic processes governed the assembly in artificial sea embankment wetlands (SEW). The presence of Spartina alterniflora in all soil types (except SEW soils) indicated stochastic assembly, while Phragmites australis in reclaimed soils pointed toward deterministic microbial assembly. Furthermore, environmental factors such as pH, soil water content (SWC), SOC, total carbon (TC), total nitrogen (TN), total phosphorus (TP), NH4+-N, vegetation types, soil depth, and geographic distance exhibited significant effects on microbial beta diversity indices. Co-occurrence network analysis revealed a stronger association between taxa in SEW compared to land reclaimed from wetlands (LRW) and natural coastal wetlands (NCW). The bottom soil layer exhibited more complex network interactions than the topsoil layer. Besides soil parameters, reclamation and varieties of vegetation were also substantial factors influencing the composition, diversity, and assembly processes of microbial communities in coastal wetlands.

Biochar and Chlorella increase rice yield by improving saline-alkali soil physicochemical properties and regulating bacteria under aquaculture wastewater irrigation

The combined effects of biochar and Chlorella under aquaculture wastewater irrigation in improving saline-alkali soil physicochemical properties, microbial communities, and rice yield, is not yet clear. This study utilized soil physicochemical indicators and gene sequencing to examine the effect of salinity stress, biochar and Chlorella under aquaculture wastewater irrigation on soil properties, bacterial community compositions, and rice production. Treatments included three factors in a randomized complete block design with three replications: (i) Biochar - 40 tons ha -1 (BW) versus no-biochar (BN); (ii) Salinity - 3‰ salinity (SH) versus 1‰ salinity (SL); and (iii) Chlorella - with 107 cells mL -1 Chlorella (CW) versus no-Chlorella (CN). The results revealed that increased salinity adversely affected the soil nutrients (TOC, NO3⁻-N, NH4+-N, Olsen-P), and enzyme activity (urease, sucrase, catalase), resulting in a 9.67% reduction in rice yield compared to SL treatment. However, the close correlation between alterations in soil bacterial communities, functions, and soil physicochemical properties, as well as rice yield, indicated that biochar and Chlorella promoted rice yield by enhancing the physicochemical properties of saline-alkali soil and bacterial community when irrigated with aquaculture wastewater: (1) addition of biochar increased the146.05% rice yield by increasing TOC content, the complexity of bacterial co-occurrence patterns, nitrogen fixation potential, and nitrification potential, (2) addition of Chlorella increased TOC, NO3⁻-N, NH4+-N, enhanced urease, sucrase, catalase activity, and nitrification potential to increased rice yield by 60.29%, and (3) compared with the treatment T3 (SHBNCN), the treatments with biochar (BW) and Chlorella (CW) increased the yield by 561.30% and 445.03% under 1‰ and 3‰ salinity, respectively. These findings provide novel perspectives on the capacity of biochar and Chlorella to improve saline-alkali soil properties and increase rice yield irrigated with aquaculture wastewater.

Conservation tillage practices affect soil microbial diversity and composition in experimental fields

Introduction

Conservation tillage is a widely used technique worldwide, but the effects of conservation tillage on bacterial community structure are poorly understood. We explored proportional alterations in the bacterial community under different tillage treatments.

Methodology

Hence, this study utilized high-throughput sequencing technique to investigate the structure and assembly processes of microbial communities in different tillage treatments.

Results and discussion

Tillage treatments included tillage no-straw retention (CntWt), no-tillage with straw retention (CntWntS), tillage with straw retention (CntWtS), no-tillage and no-straw retention (CntWnt). The influence of tillage practices on soil bacterial communities was investigated using Illumina MiSeq sequencing. Different tillage methods and straw retention systems significantly influenced soil parameters such as total potassium and pH were not affected by tillage practices, while straw retention significantly affected soil parameters including nitrogen content, available phosphorus and available potassium. Straw retention decreased bacterial diversity while increased bacterial richness. The effect of straw retention and tillage on bacterial communities was greater than with no tillage. Phylogenetic β-diversity analysis showed that deterministic homogeneous selection processes were dominated, while stochastic processes were more pronounced in tillage without straw retention. Ecological network analysis showed that microbial community correlation was increased in CntWntS and CntWnt. Straw retention treatment significantly increased the relative abundance of bacterial taxa Proteobacteria, Bacteroidetes, and OD1, while Nitrospirae, Actinobacteria, and Verrucomicrobia significantly decreased.

Conclusion

The conservation tillage practices significantly affect soil properties, bacterial composition, and assembly processes; however, further studies are required to investigate the impact of different crops, tillage practices and physiological characteristics on bacterial community structure and functions.

Bacterial community are more susceptible to nanoplastics than algae community in aquatic ecosystems dominated by submerged macrophytes

As a ubiquitous emerging pollutant, microplastics can interact with algal and bacterial communities in aquatic ecosystems. Currently, knowledge on how microplastics influence algae/bacteria is mostly limited to toxicity tests using either monocultures of algae/bacteria or specific algal-bacterial consortium. However, information on the effect of microplastics on algal and bacterial communities in natural habitats is not easily available. Here, we conducted a mesocosm experiment to test the effect of nanoplastics on algal and bacterial communities in aquatic ecosystems dominated by different submerged macrophytes. The community structure of algae and bacteria suspended in the water column (planktonic) and attached to the surface of submerged macrophytes (phyllospheric) were identified, respectively. Results showed that both planktonic and phyllospheric bacteria were more susceptible to nanoplastics, and these variations driven by decreased bacterial diversity and increased abundance of microplastic-degrading taxa, especially in aquatic systems dominated by V. natans. The community composition of both algae and bacteria were influenced to varying degrees by nanoplastics and/or plant types, but RDA results showed that only bacterial community composition was strongly correlated with environmental variables. Correlation network analysis showed that nanoplastics not only reduced the intensity of associations between planktonic algae and bacteria (average degree reduced from 4.88 to 3.24), but also reduced proportion of positive correlations (from 64% to 36%). Besides, nanoplastics also decreased the algal/bacterial connections between planktonic and phyllospheric habitats. Our study elucidates the potential interactions between nanoplastics and algal-bacterial community in natural aquatic ecosystems. These findings suggest that in aquatic ecosystems, bacterial community are more vulnerable to nanoplastics and may serve as a protective barrier for algae community. Further research is needed to reveal the protective mechanism of bacteria against algae at the community level.

Development and Determinants of Topsoil Bacterial and Fungal Communities of Afforestation by Aerial Sowing in Tengger Desert, China

It was previously reported that afforestation in the desert can help improve soil texture, carbon accumulation, and nutrient status. However, the effects of afforestation on soil microbial composition, diversity, and microbial interactions with soil physicochemical properties have been rarely evaluated quantitatively. Using the method of space-for-time substitutions, we assessed the development and determinants of topsoil bacterial and fungal communities over nearly 40 years of successive afforestation by aerial sowing in Tengger Desert, China. The results showed that afforestation by aerial sowing comprised a considerable proportion of Chloroflexi and Acidobacteria in the bacterial community in addition to the ubiquitous phyla found in desert but had fewer effects on the dominant phyla of the fungal community. At the phylum level, the bacterial community was clearly clustered into two groups. However, it was difficult to differentiate the constituents of the fungal community based on principal coordinate analysis. The richness of the bacterial and fungal communities was significantly higher after five years than at zero years and three years. Additionally, the bacterial community varied parabolically and reached its largest size at twenty years, while the fungal community increased exponentially. Soil physicochemical properties were found to have divergent effects on the abundance and diversity of bacterial and fungal communities, among which salt- and carbon-associated properties (e.g., electrical conductivity, calcium, magnesium, total carbon, and organic carbon) were closely related with the abundance of bacterial-dominant phyla and the diversity of bacteria and fungi, but nutrient-associated properties (e.g., total phosphorus and available phosphorus) were not. The results indicate that afforestation through the salt secretions of plants leaves and carbon inputs from litter promote the development of topsoil bacterial and fungal communities in the desert.

Effects of Coumarin on Rhizosphere Microbiome and Metabolome of Lolium multiflorum

Rhizosphere microorganisms can help plants absorb nutrients, coordinate their growth, and improve their environmental adaptability. Coumarin can act as a signaling molecule that regulates the interaction between commensals, pathogens, and plants. In this study, we elucidate the effect of coumarin on plant root microorganisms. To provide a theoretical basis for the development of coumarin-derived compounds as biological pesticides, we determined the effect of coumarin on the root secondary metabolism and rhizosphere microbial community of annual ryegrass (Lolium multiflorum Lam.). We observed that a 200 mg/kg coumarin treatment had a negligible effect on the rhizosphere soil bacterial species of the annual ryegrass rhizosphere, though it exhibited a significant effect on the abundance of bacteria in the rhizospheric microbial community. Under coumarin-induced allelopathic stress, annual ryegrass can stimulate the colonization of beneficial flora in the root rhizosphere; however, certain pathogenic bacteria, such as Aquicella species, also multiply in large numbers in such conditions, which may be one of the main reasons for a sharp decline in the annual ryegrass biomass production. Further, metabolomics analysis revealed that the 200 mg/kg coumarin treatment triggered the accumulation of a total of 351 metabolites, of which 284 were found to be significantly upregulated, while 67 metabolites were significantly downregulated in the T200 group (treated with 200 mg/kg coumarin) compared to the CK group (control group) (p < 0.05). Further, the differentially expressed metabolites were primarily associated with 20 metabolic pathways, including phenylpropanoid biosynthesis, flavonoid biosynthesis, glutathione metabolism, etc. We found significant alterations in the phenylpropanoid biosynthesis and purine metabolism pathways (p < 0.05). In addition, there were significant differences between the rhizosphere soil bacterial community and root metabolites. Furthermore, changes in the bacterial abundance disrupted the balance of the rhizosphere micro-ecosystem and indirectly regulated the level of root metabolites. The current study paves the way towards comprehensively understanding the specific relationship between the root metabolite levels and the abundance of the rhizosphere microbial community.

Characteristics and origin of clogging-functional bacteria during managed aquifer recharge: A laboratory study

Owing to serious influences on well performance, bacteria-induced clogging has become a dilemma for managed aquifer recharge (MAR). During MAR, surface river water is inoculated into aquifer and mixed with groundwater. Therefore, the clogging-functional bacteria may originate from the river water or the groundwater. However, the origin of the clogging-functional bacteria in the aquifer has not yet been well understood. This study conducted a series of laboratory-scale column experiments involving different recharge modes (using river water, groundwater) to simulate the processes of bacteria-induced clogging and used the high-throughput sequencing technology, aiming to elucidate the community characteristics and the origin of the clogging-functional bacteria involved in MAR bioclogging. Analyses of the bacterial-community characteristics showed significant differences between the river water and groundwater. The bacterial-community characteristics of the clogging aquifer in the different recharge modes were similar to each other and have common genera, namely, Acinetobacter, Brevundimonas, Exiguobacterium, Porphyrobacter, Cloacibacterium, and Sphingobium, which suggests that MAR activity could promote bacterial communities to become identical during surface water infiltration into aquifers, despite differences in the bacterial communities present in the subsurface- and surface systems. This knowledge will assist greatly in targeted treatment and prophylaxis of clogging-functional bacteria during managed aquifer recharge.

Succession of soil bacterial community along a 46-year choronsequence artificial revegetation in an arid oasis-desert ecotone

How the bacterial community structure and potential metabolic functions will change after revegetation in arid desert ecosystems is still unknown. We used high-throughput pyrosequencing to explore changes in soil bacterial diversity, structure and metabolic pathways, and the key driving factors along a chronosequence of 46-year Haloxylon ammodendron revegetation in an oasis-desert ecotone in the northwestern China. Our results indicated that establishment of H. ammodendron on shifting sand dunes significantly changed the structure of bacterial communities and increased their diversity and richness. The main dominant phyla were Actinobacteria (32.1-41.3%) and Proteobacteria (19.2-27.0%); in that, α-Proteobacteria (16.4-20.7%) were the most abundant Proteobacteria. Kocuria coexisted at different succession stage after year 0, and their relative abundance ranged from 3.8-9.0%. Principal coordinates analysis (PCoA) showed that bacterial community from the same revegetation site grouped together and generally separated from each other, indicating that significant shifts in bacterial community structure occurred after revegetation. LEfSe analysis identified unique biomarkers in the soil samples from seven sites. Moreover, PICRUSt analysis indicated similar overall patterns of metabolic pathways in different succession stage. Redundancy analysis (RDA) showed that total carbon, pH and total phosphorus were major abiotic factors driving the structure of bacterial communities, which explained 57.5% of the variation in bacterial communities. Our findings advance the current understanding of plant-soil interactions in the processes of ecological restoration and desertification reversal.

The rhizosphere effect of native legume Albizzia julibrissin on coastal saline soil nutrient availability, microbial modulation, and aggregate formation

In the coastal zones, numerous ecological shelterbelt projects were conducted to protect against natural hazards. However, it is still not fully understood whether phytoremediation with native legume Albizzia julibrissin plantation can improve saline soil structural development or microbial community structure. In this study, a field experiment was conducted to investigate the responses of rhizosphere soil salinity, nutrients, bacterial community, and aggregate structure to A. julibrissin plantation in a recently reclaimed area along Zhejiang coast, China. After ~3-year plantation, rhizosphere soil pH and EC reduced to 8.25 and 0.14 dS·m^-1, respectively, belonging to non-saline soil. Meanwhile, total organic carbon (TOC), permanganate-oxidizable carbon (POXC), total nitrogen (TN), alkali-hydrolyzable nitrogen (AN), and ammonium nitrogen (NH₄⁺-N) were significantly increased in rhizosphere soil compared with bare land (P < 0.05). Consequently, rhizosphere soil had favorable habitat condition for copiotrophic bacterial taxa (e.g., Chloroflexi, Acidobacteria, and Bacteroidates), as well as high diversity, complex co-occurrence network, and catabolism related with nutrient cycling. The soil particle size of bare land was < 0.053 mm, while microaggregate (0.053-0.25 mm) and macroaggregate (0.25-2 mm) were formed in the rhizosphere and coupled with C accumulation and Fe removal. Soil aggregates were of great importance to soil fertility with more efficient bacterial network and biogeochemical cycles of nutrients. N-fixing Rhizobiales preferred to inhabit large soil particle and might primarily contribute to N accumulation. Generally, A. julibrissin was a suitable pioneer tree for mudflat reclamation projects, which effectively improved saline soil rhizosphere environment by reducing salinity, accumulating C and N, and promoting microbial community succession, as well as aggregate structure formation.

Short-Term Effects of Reclamation of Aquaculture Ponds to Paddy Fields on Soil Chemical Properties and Bacterial Communities in Eastern China Coastal Zone

Large areas of tidal flats were previously developed into aquaculture ponds and were recently encouraged to be converted into paddy fields to fulfill food and economic needs in China. However, the influences of short-term rice cultivation at the reclaimed aquaculture ponds on soil chemical properties and bacterial communities are poorly understood. To address this issue, we collected mineral soil samples at 0–20 and 20–40 cm depths from non-cultivated soils and paddy fields after being reclaimed from aquaculture ponds in Nantong, China, and identified soil bacterial communities using high-throughput sequencing. The results suggested that rice cultivation significantly increased the accumulation of total soil carbon (TC) and dissolved organic carbon (WSOC). The pH, ammonium (NH4+), nitrate (NO3−) and available phosphorus (AP) varied with the reclamation duration but did not show a unanimous tendency. Proteobacteria, Acidobacteria, Bacteroidetes, Chloroflexi and Planctomycetes dominated the bacterial community in both non-cultivated and cultivated soils after reclamation regardless of cultivation ages and soil depth. The variations in the diversity and composition of the soil microbial community were mainly associated with electrical conductivity (EC), WSOC, TC, NH4+ and NO3− in non-cultivated and cultivated lands. Here, we found that short-term rice cultivation at the reclaimed aquaculture ponds strongly influenced soil bacterial communities and chemical properties, especially in the 0–20 cm depth, in the coastal regions.

Effect of the Nanoparticle Exposures on the Tomato Bacterial Wilt Disease Control by Modulating the Rhizosphere Bacterial Community

Ralstonia Solanacearum is one of the most infectious soil-borne bacterial plant pathogens, causing tomato bacterial wilt (TBW). Nanotechnology is an emerging area of research, particularly the application of nanoparticles (NPs) as nanopesticides to manage plant disease is gaining attention nowadays. However, the interaction between NPs and rhizosphere bacterial communities remains largely elusive. This study indicated that metal NPs (CuO, ZnO, and FeO) reduced the incidence of bacterial wilt to varying degrees and affected the composition and structure of the rhizosphere bacterial community. The results revealed that the application of metal oxide NPs can improve the morphological and physiological parameters of TBW infected tomato plants. Among all, CuONPs amendments significantly increase the Chao1 and Shannon index. In the early stage (the second week), it significantly reduces the relative abundance of pathogens. However, the relative abundance of beneficial Streptomyces bacteria increased significantly, negatively correlated with the relative abundance of pathogenic bacteria. In addition, the nano-treatment group will enrich some potential beneficial bacteria such as species from Sphingomonadaceae, Rhizobiaceae, etc. In general, our research provides evidence and strategies for preventing and controlling soil-borne disease tomato bacterial wilt with metal oxide NPs.

Rhizosphere bacteria community and functions under typical natural halophyte communities in North China salinized areas

Soil salinity is a serious environmental issue in arid China. Halophytes show extreme salt tolerance and are grow in saline-alkaline environments. There rhizosphere have complex bacterial communities, which mediate a variety of interactions between plants and soil. High-throughput sequencing was used to investigated rhizosphere bacterial community changes under the typical halophyte species in arid China. Three typical halophytes were Leymus chinensis (LC), Puccinellia tenuiflora (PT), Suaeda glauca (SG). The dominant phyla were Proteobacteria, Actinobacteria, Chloroflexi, Gemmatimonadetes, Acidobacteria and Bacteroidetes, Suaeda glauca rhizosphere has stronger enrichment of Nitrospirae and Cyanobacteria. The Ace, Chao and Shannon indices were significantly higher in soils under LC and SG (P<0.05). Functional predictions, based on 16S rRNA gene by PICRUSt, indicated that Energy metabolism, Amino acid metabolism, Carbohydrate metabolism and Fatty acid metabolism are dominant bacterial functions in three halophytes rhizosphere soil. Carbon metabolism, Oxidative phosphorylation, Methane metabolism, Sulfur metabolism and Nitrogen metabolism in SG were significantly higher than that in LC and PT. Regression analysis revealed that rhizosphere soil bacterial community structure is influenced by soil organic matter (SOM) and soil water content (SWC), while soil bacterial community diversity is affected by soil pH. This study contributes to our understanding of the distribution characteristics and metabolic functions under different halophyte rhizosphere bacterial communities, and will provide references for the use of rhizosphere bacteria to regulate the growth of halophytes and ecological restoration of saline soil.

Response of Soil Properties and Microbial Communities to Increasing Salinization in the Meadow Grassland of Northeast China

Secondary salinization is a serious environmental issue and a major threat to the sustainable use of grasslands. Information about the response of microbial communities and soil properties in already saline soils to increasing salinity is lacking. We investigated soil properties and the structures of soil bacterial and fungal communities across a gradient of salinization in the Horqin Grassland, China. Three sites with relatively lightly (average soluble salt content = 0.11%), relatively moderately (average soluble salt content = 0.44%), and heavily (average soluble salt content = 1.07%) degraded grassland, were selected as experimental sites. We examined variations in the composition and structure of the soil bacterial and fungal communities by using high-throughput sequencing of the 16S and 18S rRNA genes, respectively. We found degrading effects of salinization on soil properties, i.e., decreased soil moisture, organic matter, total N, NH₄-N, and NO₃-N and increased soil bulk density, pH, and electrical conductivity. The bacterial and fungal community structures changed with increasing salinity. However, dominant microbial taxa (including phylum, genus, and operational taxonomic unit levels) were similar among experimental sites, indicating that increasing salinization slightly affected the basic compositions of microbial communities in already saline grasslands. Furthermore, the relative abundances of most dominant taxa sensitively responded to the soil salt content. Acidobacteria, Actinobacteria, Chloroflexi, RB4, Rubrobacter, Blastocatella, H16, Glomeromycota, and Aspergillus linearly increased with increasing salinization, suggesting that they could be used as bioindicators for salt-tolerant communities. Overall, the changes in the structures of soil bacterial and fungal communities were determined by the relative quantities of dominant taxa rather than community composition. The structures of soil bacterial and fungal communities were linked to soil properties and vegetation. Increasing soil salt content, and thereby varied pH and organic matter, were likely the direct influencing factors of microbial communities in these saline grasslands.

Long-Term Chili Monoculture Alters Environmental Variables Affecting the Dominant Microbial Community in Rhizosphere Soil

Continuous cropping negatively affects soil fertility, physicochemical properties and the microbial community structure. However, the effects of long-term chili monoculture on the dominant microbial community assembly are not known. In this study, the impact of long-term chili monoculture on the correlation between the dominant microbial community and soil environmental variables was assessed. The results indicated that increasing duration of chili monoculture generated significant changes in soil nutrients, soil aggregates and soil enzymes: nutrient contents increased overall, mechanically stable macroaggregates increased and microaggregates decreased, water-stable macroaggregates and microaggregates decreased, β-glucosidase decreased nonlinearly, and nitrate reductase and alkaline phosphatase activities showed a nonlinear increase. Moreover, an increasing number of years of chili monoculture also affected the structure of the dominant microbiota, with substantial changes in the relative abundances of 11 bacterial and fungal genera. The drivers of the dominant microbial community assembly in rhizosphere soil were soil moisture, abiotic nitrogen, pH and salt.

Soil Bacterial Community Response and Nitrogen Cycling Variations Associated with Subalpine Meadow Degradation on the Loess Plateau, China

Grassland degradation is an ecological problem worldwide. This study aimed to reveal the patterns of the variations in bacterial diversity and community structure and in nitrogen cycling functional genes along a subalpine meadow degradation gradient on the Loess Plateau, China. Meadow degradation had a significant effect on the beta diversity of soil bacterial communities (P < 0.05) but not on the alpha diversity (P > 0.05). Nonmetric multidimensional scaling (NMDS) and analysis of similarity (ANOSIM) indicated that the compositions of bacterial and plant communities changed remarkably with increasing meadow degradation (all P < 0.05). The beta diversities of the plant and soil bacterial communities were significantly correlated (P < 0.05), while their alpha diversities were weakly correlated (P > 0.05) along the meadow degradation gradient. Redundancy analysis (RDA) showed that the structure of the bacterial community was strongly correlated with total nitrogen (TN), nitrate nitrogen (NO₃ ^--N), plant Shannon diversity, plant coverage, and soil bulk density (all P < 0.05). Moreover, the abundances of N fixation and denitrification genes of the bacterial community decreased along the degradation gradient, but the abundance of nitrification genes increased along the gradient. The structure of the set of N cycling genes present at each site was more sensitive to subalpine meadow degradation than the structure of the total bacterial community. Our findings revealed compositional shifts in the plant and bacterial communities and in the abundances of key N cycling genes as well as the potential drivers of these shifts under different degrees of subalpine meadow degradation.IMPORTANCE Soil microbes play a crucial role in the biogeochemical cycles of grassland ecosystems, yet information on how their community structure and functional characteristics change with subalpine meadow degradation is scarce. In this study, we evaluated the changes in bacterial community structure and nitrogen functional genes in degraded meadow soils. Meadow degradation had a significant effect on bacterial community composition. Soil total nitrogen was the best predictor of bacterial community structure. The beta diversities of the plant and soil bacterial communities were significantly correlated, while their alpha diversities were only weakly correlated. Meadow degradation decreased the potential for nitrogen fixation and denitrification but increased the potential for nitrification. These results have implications for the restoration and reconstruction of subalpine meadow ecosystem on the Loess Plateau.

Responses of the rhizosphere bacterial community in acidic crop soil to pH: Changes in diversity, composition, interaction, and function

Soil pH is an important predictor of bacterial community composition and diversity. Examining the effects of pH on diversity, structure, interaction, and function of rhizosphere bacterial communities in acidic crop soils provide valuable information for knowing potential role of rhizosphere bacteria in crop yield. Here, we collected soils from artificial greenhouses and applied Illumina Miseq sequencing, quantitative PCR techniques, multiple ecological analysis methods, including topological analysis and functional profiling to analyze our data and validate our hypotheses. We found that the soil physicochemical properties, species diversity, and rhizosphere bacterial community composition were significantly affected by the degree of soil acidification (pH < 5.5 and pH > 5.5) but not vegetation type. Additionally, bacterial absolute abundance increased with higher pH. The 18 soil samples were clustered into two distinct groups of pH < 5.5 and pH > 5.5 at the OTU level, and soil pH had more of an effect on bacterial community composition compared to the other physicochemical variables. In addition, rhizosphere bacteria might presented relatively less competition for survival in pH < 5.5 soils, and bacterial community functions, including nutrient (i.e., carbon, nitrogen, phosphorus, and sulphur) cycling-related enzymes and proteins, were downregulated in more acidic soils (pH < 5.5) based on sequence analysis. To our knowledge, this report is the first to show that pH is a key factor affecting the diversity, structure, interaction, and function of rhizosphere bacterial communities in acidic crop soil in artificial greenhouses. Our findings emphasize that community function and structure of rhizosphere bacteria are closely correlated in more acidic soils, and the decreased crop yield may be correlated with attenuation of the function of the rhizosphere bacterial community.

Metabarcoding reveals differences in fungal communities between unflooded versus tidal flat soil in coastal saline ecosystem

In the saline-affected ecosystem, fungi have huge potential to promote growth, induce disease resistance and enhance tolerance against salt-stress of host plants. Since areas of plowland are gradually decreasing, the reclamation of coastal saline lands could play a crucial role in maintaining agricultural productivity and crop security globally. Therefore, it is of great significance to explore the fungal diversity in the coastal saline ecosystem. Here, we collected saline soil samples from unflooded areas and tidal flat areas, the two typical distinct landforms in coastal saline ecosystems, and used ITS metabarcoding to depict the diversity of fungal communities. We found that fungal species evenness had a remarkably higher variation from the tidal flat compared to unflooded soil samples. Furthermore, we also confirmed that the fungal niches differentiation reports in the coastal saline ecosystem. Our ITS based DNA sequencing revealed that both unflooded and tidal flat soil were mainly composed of amplicon sequence variants (ASVs) belonging to Ascomycota (93.43% and 86.91% respectively). Based on our findings, understanding the associations and distinctions of fungal microbiome between unflooded soil and tidal flat could provide the basis for the development of reclamation in coastal saline lands.

Effect of aridity and dune type on rhizosphere soil bacterial communities of Caragana microphylla in desert regions of northern China

Understanding the response of soil properties and bacterial communities in rhizosphere soil to aridity and dune types is fundamental to desertification control. This study investigated soil properties and bacterial communities of both rhizosphere and bulk soils of Caragana microphylla from four sites with different aridity indices, and one site with three different types of dunes. All sites were located in the desert regions of northern China. The results indicated that compared with the bulk soil, the soil nutrient content of rhizosphere, especially the content of total phosphorus, was generally significantly improved in different desertification environments. The bacterial richness and diversity were also higher than those of bulk soil, especially in arid regions and fixed dunes. Firmicutes, Actinobacteria, Proteobacteria, and Acidobacteria were the most dominant phyla in all samples. The regression analyses showed that at different sites, soil total organic C, total N, Na⁺, and total P played key roles in determining the bacterial community structure while total organic carbon, electronic conductivity, pH and total phosphorus were the dominant factors at the different dunes. The results further revealed that the dominant phyla strongly affected by environmental factors at different sites were Acidobacteria, Gemmatimonadetes, and Actinobacteria among which, Acidobacteria and Gemmatimonadetes were negatively correlated with Na⁺ content. At different types of dunes, Actinobacteria, Planctomycetes, and Gemmatimonadetes were particularly affected by environmental factors. The increased abundance of Actinobacteria in the rhizosphere soil was mainly caused by the decreased soil pH.

Vertical response of microbial community and degrading genes to petroleum hydrocarbon contamination in saline alkaline soil

A column microcosm was conducted by amending crude oil into Dagang Oilfield soil to simulate the bioremediation process. The dynamic change of microbial communities and metabolic genes in vertical depth soil from 0 to 80 cm were characterized to evaluate the petroleum degradation potential of indigenous microorganism. The influence of environmental variables on the microbial responds to petroleum contamination were analyzed. Degradation extent of 42.45% of n-alkanes (C8-C40) and 34.61% of 16ΣPAH were reached after 22 weeks. Relative abundance of alkB, nah, and phe gene showed about 10-fold increment in different depth of soil layers. Result of HTS profiles demonstrated that Pseudomonas, Marinobacter and Lactococcus were the major petroleum-degrading bacteria in 0-30 and 30-60 cm depth of soils. Fusarium and Aspergillus were the dominant oil-degrading fungi in the 0-60 cm depth of soils. In 60-80 cm deep soil, anaerobic bacteria such as Bacteroidetes, Lactococcus, and Alcanivorax played important roles in petroleum degradation. Redundancy analysis (RDA) and correlation analysis demonstrated that petroleum hydrocarbons (PHs) as well as soil salinity, clay content, and anaerobic conditions were the dominant effect factors on microbial community compositions in 0-30, 30-60, and 60-80 cm depth of soils, respectively.