Soil Bacterial Community Composition Research Articles

Decomposing benefits: Examining the impact of beech deadwood on soil properties and microbial diversity

Deadwood is an important element of forest ecosystems that affects many of its components, including the soil environment. Our research is an attempt to determine the role of decaying wood in shaping the properties of forest soils in mountain ecosystems. The aim of our research was to present the influence of beech deadwood on physicochemical properties and microbiological diversity of soils. The research was carried out in the Baba Góra Massif at its northern exposure. The research plots were established in the altitude gradient at 600, 800 and 1000 m above sea level. On each plot, samples were taken from decaying wood, from the soil directly under the decaying log, and a soil sample 1 m from the log as a control. We determined the basic properties of the samples, that is pH, C and N concentration and lignin content. The enzymatic activity and additionally, the taxonomic composition of soil bacterial and fungal communities was determined in the collected samples. Our research indicates the important role of decaying beech wood in shaping the properties of forest soils. We noted a positive effect of decaying wood on the properties of the tested soils. Soils affected by deadwood were characterized by significantly higher pH, C and N concentrations compared to control soils, regardless of their location in the altitude gradient. Additionally, we found that soils affected by decaying wood are characterized by a different composition of microorganisms regardless of their location in the altitude gradient. In control soil the fungal and bacterial alpha diversity were lowest compared with the deadwood and soil under the influence of deadwood. Our results may have practical applications in the management of forest ecosystems. The presented results indicate the possibility of leaving deadwood in order to improve its basic physicochemical properties and increase microbial diversity.

Comparative Analysis of Biodegradable Mulches on Soil Bacterial Community and Pepper Cultivation

Biodegradable mulch films (BMFs) are becoming increasingly popular in agricultural practices. However, research on the ecological impact of biodegradable mulch films on pepper–soil systems is still scarce. To compare the differential effects of BMFs and polyethylene (PE) mulch on soil chemical properties, soil bacterial community composition, and pepper cultivation, a study was conducted encompassing eight distinct treatments. These treatments included three varieties of polybutylene adipate terephthalate (PBAT) combined with polylactic acid (PLA) mulches: PP-JL, PP-SD, and PP-SH; a black polypropylene carbonate mulch (PPC-BK); a brown PPC mulch (PPC-BR); a polyethylene (PE) mulch; straw mulching (NCK); and an uncovered control (PCK). After applying mulches for 129 days, most PPC and PBAT + PLA films had reached the rupture phase, whereas the PE film was still in the induction phase. Pepper yield was obviously higher in all mulched treatments (4830 kg hm−1) than in the un-mulched control (3290 kg hm−1), especially the BMF PP-JL treatment, which showed the most notable improvements in yield. Although BMF treatments maintained a lower soil temperature than the PE film mulch, they were still higher than the un-mulched control. Furthermore, the soil bacterial community composition and ecological network were not markedly affected by different mulching conditions. However, the PP-SH treatment significantly increased the abundance of Pseudomonas, Nitrosomonas, and Streptomyces genera. Moreover, Lactobacillus and Gp16 were substantially more abundant in the PPC-black (BK) and PPC-brown (BR) treatments compared to the PE mulching treatment. This study could provide valuable insights into the ecological benefits of BMFs in pepper cultivation. However, as our experiments were conducted for only one season, it is imperative to undertake long-term experiments across consecutive seasons and years for a thorough understanding and comprehensive study.

Soil Fertility and Bacterial Community Composition in Response to the Composting of Biochar-Amended Chicken Manure

Amidst the burgeoning expanse of the poultry sector, the escalation of chicken manure production has ensued, potentially exacerbating ecological contamination. However, the application of chicken manure is bound to transmute the habitat of edaphic microorganisms, precipitating an alteration in the soil’s microbial consortium. The composting of biochar-amended chicken manure and wood chips (biochar composting products, BCPs) was used to improve Chinese cabbage (Brassica campestris L.) production and regulate soil properties and bacterial community structure. On the 40th day of Chinese cabbage growth, soil and Chinese cabbage were collected for laboratory analysis. The effects of different proportions of BCPs (0, 1%, 3%, 5% and 7% biochar) on soil fertility, enzyme activity, the microbial community and the growth of Chinese cabbage were studied under facility conditions. The results showed that the growth performance and quality of Chinese cabbage were significantly increased with increasing BCP ratios. Soil fertility indicators including pH, AN, AP, AK and SOM were significantly increased, except for the pH value in the 1% BCP group. The activities of phosphatase, catalase and urease were increased for all groups of BCP treatment. The soil microbial community response was significantly different, and the application of 5% and 7% BCPs reduced the abundance, diversity and evenness of soil bacteria. Chinese cabbage growth performance was positively correlated with an increase in BCP supplemental levels in the range of 3–5%. Also, the abundance, diversity and uniformity of the soil microbial community were improved in the 3% BCP treatment group. Therefore, the dominant bacterial phyla were Bacteroidetes, Actinobacteriota, Gemmatimonadota, Myxococcota, Bdellovibrionota and Firmicutes, especially the Bradyrhizobium of Proteobacteria. BCP treatment reduced the degradation of soil organic matter. In addition, it also improved the relative abundance of sequences associated with improving soil fertility. Collectively, these findings offer insights for the re-evaluation of application management strategies for BCP organic fertilizers.

Diversity and growth-promoting characteristics of rhizosphere bacteria of three naturally growing plants at the sand iron ore restoration area in Qinghe County

It is a great challenge to restore northern mines after mining and achieve optimal results due to the extremely harsh environment and climate, as in Qinghe County of Xinjiang Province, China. Qinghe County has a climate of drought, cold, strong winds, and high altitude. After sand and iron mining, the soil in this area contains a large amount of sand and gravel with extremely low organic matter, nitrogen deficiency, and a high pH of 9.26. Our preliminary studies disclosed that only three plants, including Caligonum junceum, Atraphaxis virgata, and Melilotus albus Medic, can grow naturally in this environment without any artificial management. For effective ecology restoration, this study explored the mechanism of plant-microbial interaction and stress resistance in this environment. It was found that although the soil condition in the sand iron ore landfill area is extreme, the bacterial diversity remained high, with Shannon and Simpson indices reaching 9.135 and 0.994, respectively. The planting of three types of remediation plants did not significantly improve, or even decreased, the soil bacterial diversity index, but greatly changed the composition of dominant bacterial genera. Significant differences in the composition of rhizosphere soil bacterial communities among these three remediation plants were observed. Potential new bacterial species accounted for 9.8 %, and the proportion of unique genera reached 30 % or 50 %, respectively. Among all the isolated strains, 74 % had nitrogen fixation and other growth-promoting properties. In summary, the soil microbial community structure in this extreme environment is unique and diverse. The types of remediation plants play a major role in the composition of the rhizosphere bacterial community structure, and the recruited growth-promoting bacteria are diverse and functional. This study may offer valuable information for further studies in vegetation restoration and aid in ecology restoration, especially under extreme conditions.

Organic Fertilizer with High Nutrient Levels Affected Peanut-Growing Soil Bacteria More Than Fungi at Low Doses

The breeding of laying hens and broilers in China has increased tremendously. Wet organic fertilizer prepared from hen manure using high-temperature container fermentation preserves high levels of nutrients and a diverse microbial community. We applied low doses of organic fertilizer to peanuts in the black soil area of China’s northeastern region. Based on the calculation of nitrogen content, treatments were set as follows: chemical fertilizer (PCF), organic fertilizer (POF, 4500 kg·ha−1), and replacement of 50% chemical fertilizer with organic fertilizer (PR, 2250 kg·ha−1). Compared to the plots with chemical fertilizers, the use of organic fertilizer and replacing 50% of the chemical fertilizers with organic fertilizer significantly increased peanut yields. Both the organic fertilizer and replacing 50% of the chemical fertilizers with organic fertilizer did not significantly affect the activities of the most tested soil enzymes related to carbon transformation and the absolute abundance of microorganisms. However, they did significantly enhance soil dehydrogenase and α-glucosidase. The community abundance ratio of fungi/bacteria trended downward, leading to soil with a high-fertility bacterial composition. The replacement of 50% chemical fertilizer with organic fertilizer significantly enhanced the species richness and diversity of the bacterial and fungal communities. Organic fertilizer treatment significantly increased the relative abundance of Gemmatimonas and Sphingomonas. The relative abundance of Mycobacterium in the treatment where 50% of the chemical fertilizers were replaced with organic fertilizer was significantly lower than that in the organic fertilizer treatment. PCoA results showed that the low-dose organic fertilizer treatment, replacing 50% of the chemical fertilizers with organic fertilizer, had a significant impact on the composition of soil bacterial communities.

Childcare centre soil microbiomes are influenced by substrate type and surrounding vegetation condition

Urban development has profoundly reduced human exposure to biodiverse environments, which is linked to a rise in human disease. The ‘biodiversity hypothesis’ proposes that contact with diverse microbial communities (microbiota) benefits human health, as exposure to microbial diversity promotes immune training and regulates immune function. Soils and sandpits in urban childcare centres may provide exposure to diverse microbiota that support immunoregulation at a critical developmental stage in a child's life. However, the influence of outdoor substrate (i.e., sand vs. soil) and surrounding vegetation on these environmental microbiota in urban childcare centres remains poorly understood. Here, we used 16S rRNA amplicon sequencing to examine the variation in bacterial communities in sandpits and soils across 22 childcare centres in Adelaide, Australia, plus the impact of plant species richness and habitat condition on these bacterial communities. We show that sandpits had distinct bacterial communities and lower alpha diversity than soils. In addition, we found that plant species richness in the centres' yards and habitat condition surrounding the centres influenced the bacterial communities in soils but not sandpits. These results demonstrate that the diversity and composition of childcare centre sandpit and soil bacterial communities are shaped by substrate type, and that the soils are also shaped by the vegetation within and surrounding the centres. Accordingly, there is potential to modulate the exposure of children to health-associated bacterial communities by managing substrates and vegetation in and around childcare centres.

Differential response patterns of soil fungal and bacterial communities to typical vegetation types in the Yellow River floodplain ecosystem

Soil microorganisms are one of the primary driving factors of biogeochemical cycles in floodplain ecosystems. Vegetation type has an impact on the activities of soil microorganisms. However, it is currently unclear whether the composition and structure of soil bacterial and fungal communities in floodplain ecosystems have a consistent response pattern to vegetation communities. In this research, Illumina Mi-Seq sequencing technology was employed to study the soil fungal and bacterial communities covered by three typical vegetation communities in the Yellow River floodplain ecosystem. Our results showed that the underground biomass, total carbon (TC) and nitrogen (TN) were significantly different between the three vegetation communities. In the surface soil of summer, the Shannon index of fungi community was the highest in Tamarix chinensis (T. chinensis) and the lowest in Phragmites australis (P.australis). In autumn, the Shannon and Simpson indices of bacterial communities in surface soil were the highest in the P.australis and the lowest in the Sonchus arvensis (S.arvensis), but there was no significant difference in the β-diversity of bacterial community among the three vegetation communities. In autumn, the Chao1 index of fungal community in subsoil was the highest in P.australis and the lowest in S.arvensis, while there was no significant difference in the α-diversity of bacterial community among the three vegetation communities. In addition, there were considerable disparities in the fungal and bacteria community structure in various vegetation soils. Redundancy analysis (RDA analysis) showed that TN, TC, AP, pH, NO3 -, NH4 + and moisture content were key factors driving bacterial community structure, while TP, NH4 +, pH and moisture content were essential factors driving fungal community composition. These outcomes help to improve our understanding of the ecological model of soil fungal and bacterial community in floodplain ecosystems and give assistance in improving the role of an ecological barrier and floodplain service possibilities.

Effect of Biogas Slurry on the Soil Properties and Microbial Composition in an Annual Ryegrass-Silage Maize Rotation System over a Five-Year Period.

Soil health is seriously threatened by the overuse of chemical fertilizers in agricultural management. Biogas slurry is often seen as an organic fertilizer resource that is rich in nutrients, and its use has the goal of lowering the amount of chemical fertilizers used while preserving crop yields and soil health. However, the application of continuous biogas slurry has not yet been studied for its long-term impact on soil nutrients and microbial communities in a rotation system of annual ryegrass-silage maize (Zea mays). This study aimed to investigate the impacts on the chemical properties and microbial community of farmland soils to which chemical fertilizer (NPK) (225 kg ha-1), biogas slurry (150 t ha-1), and a combination (49.5 t ha-1 biogas slurry + 150 kg ha-1 chemical fertilizer) were applied for five years. The results indicated that compared to the control group, the long-term application of biogas slurry significantly increased the SOC, TN, AP, and AK values by 45.93%, 39.52%, 174.73%, and 161.54%, respectively; it neutralized acidic soil and increased the soil pH. TN, SOC, pH, and AP are all important environmental factors that influence the structural composition of the soil's bacterial and fungal communities. Chemical fertilizer application significantly increased the diversity of the bacterial community. Variation was observed in the composition of soil bacterial and fungal communities among the different treatments. The structure and diversity of soil microbes are affected by different methods of fertilization; the application of biogas slurry not only increases the contents of soil nutrients but also regulates the soil's bacterial and fungal community structures. Therefore, biogas slurry can serve as a sustainable management measure and offers an alternative to the application of chemical fertilizers for sustainable intensification.

Influences of the Integrated Rice-Crayfish Farming System with Different Stocking Densities on the Paddy Soil Microbiomes.

Integrated rice-fish farming has emerged as a novel agricultural production pattern to address global food security challenges. Aiming to determine the optimal, scientifically sound, and sustainable stocking density of red claw crayfish (Cherax quadricarinatus) in an integrated rice-crayfish farming system, we employed Illumina high-throughput 16S rRNA gene sequencing to evaluate the impact of different stocking densities of red claw crayfish on the composition, diversity, function, and co-occurrence network patterns of soil bacterial communities. The high stocking density of red claw crayfish reduced the diversity and evenness of the soil bacterial community during the mid-culture stage. Proteobacteria, Actinobacteria, and Chloroflexi emerged as the most prevalent phyla throughout the experimental period. Low stocking densities initially boosted the relative abundance of Actinobacteria in the paddy soil, while high densities did so during the middle and final stages. There were 90 distinct functional groups identified across all the paddy soil samples, with chemoheterotrophy and aerobic chemoheterotrophy being the most abundant. Low stocking densities initially favored these functional groups, whereas high densities enhanced their relative abundances in the later stages of cultivation. Medium stocking density of red claw crayfish led to a more complex bacterial community during the mid- and final culture stages. The experimental period showed significant correlations with soil bacterial communities, with total nitrogen (TN) and total phosphorus (TP) concentrations emerging as primary factors contributing to the alterations in soil bacterial communities. In summary, our findings demonstrated that integrated rice-crayfish farming significantly impacted the soil microbiomes and environmental factors at varying stocking densities. Our study contributed to theoretical insights into the profound impact of integrated rice-crayfish farming with various stocking densities on bacterial communities in paddy soils.

Effect of Forest Fires on the Alpha and Beta Diversity of Soil Bacteria in Taiga Forests: Proliferation of Rare Species as Successional Pioneers

Forest fires are among the most influential drivers of changes in forest soil bacterial diversity. Nevertheless, little is known regarding the effects of forest fires on maintaining the complex interactions that preserve forest ecosystem stability. Therefore, this study characterized alterations in soil bacterial community composition and diversity within taiga forests subjected to varying disturbance intensities. Particularly, this study examined the bacterial community within a Larix gmelinii fire-burnt site in Daxinganling, analyzing the changes in bacterial community structure and function across light, moderate, and heavy fire-burnt sites, as well as a control sample site, utilizing Illumina MiSeq technology. Through an assessment of bacterial community diversity and soil physicochemical properties (moisture content (MC), pH, microbial biomass carbon (MBC), organic carbon (SOC), total nitrogen (TN), available nitrogen (AN), available phosphorus (AP), and available potassium (AP)), we explored the influence of the soil microenvironment on the soil bacterial community structure at the burnt site under different disturbance intensities. Our findings demonstrated that (1) there was no significant change in the Chao index of soil bacteria in the burnt site under different disturbance intensities, whereas the Shannon index decreased significantly (p < 0.05) and the Simpson index increased significantly (p < 0.05) in the burnt site under light and moderate disturbance. (2) The relative abundance of dominant phyla, such as Proteobacteria, Proteobacteria, and Actinobacteriota, did not change significantly in the fire-burnt site under different disturbance intensities, whereas rare species, such as Acidipila, Occallatibacter, and Acidibacter, experienced a significant increase in relative abundance at the genus level. (3) The results of principal coordinates analysis (PCoA) and canonical correlation analysis (CCA) revealed significant differences in the Beta diversity of soil bacteria in the fire-burnt site under varying interference intensities. The Beta diversity of soil bacteria exhibited significant differences (p = 0.001), with MC, pH, TN, AN, and AK identified as significant influencing factors. (4) FAPROTAX functional prediction analyses were conducted to assess the changes in soil bacteria involved in Cellulolysis, Chemoheterotrophy, and Aerobic_Chemoheterotrophy in the fire-burnt site, with the relative abundance of bacteria involved in Chemoheterotrophy being significantly increased (p < 0.05) under different disturbance intensities. Collectively, our findings demonstrated that different disturbance intensities caused by fires significantly affected the Alpha diversity, Beta diversity, and functional abundance of soil bacterial communities in taiga forests, with MC, pH, TN, AN, and AK being identified as key influencing factors. Additionally, the presence of numerous rare species suggests their role as pioneer communities in the succession of soil bacterial communities.

Intercropping changed the soil microbial community composition but no significant effect on alpha diversity.

Enhancing the planning of the forest-agricultural composite model and increasing the efficiency with which forest land is utilized could benefit from a thorough understanding of the impacts of intercropping between forests and agriculture on soil physicochemical properties and microbial communities. Populus cathayana × candansis cv. Xinlin No.1 and Glycine max intercrop soils, along with their corresponding monocrops, were used in this study's llumina high-throughput sequencing analysis to determine the composition and diversity of soil bacterial and fungal communities. The findings indicated that intercropping considerably raised the soil's total phosphorus content and significantly lowered the soil's carbon nitrogen ratio when compared to poplar single cropping. Furthermore, the total carbon and nitrogen content of soil was increased and the soil pH was decreased. The sequencing results showed that intercropping had no significant effect on soil alpha diversity. Intercropping could increase the composition of fungal community and decrease the composition of bacterial community in poplar soil. At the phylum level, intercropping significantly increased the relative abundance of four dominant phyla, i.e., Patescibacteria, Proteobacteria, Patescibacteria and Deinococcus-Thermus. And the relative abundances of only two dominant phyla were significantly increased. It was found that soil total phosphorus and available phosphorus content had the strongest correlation with soil bacterial community diversity, and soil pH had the strongest correlation with soil fungal community diversity. The results of this study were similar to those of previous studies. This study can serve as a theoretical foundation for the development of a poplar and black bean-based forest-agricultural complex management system in the future.

Compositional and functional analysis of the bacterial community of Mediterranean Leptosols under livestock grazing

The composition and functioning of soil bacterial communities, as well as their responses to multiple perturbations, are not well understood in the terrestrial ecosystems. Our study focuses on the bacterial community of erosive and poorly developed soils (Haplic Leptosols) in Mediterranean rangelands of Extremadura (W Spain) with different grazing intensities. Leptosols from similar natural conditions were selected and sampled at two depths to determine the soil properties as well as the structure and activity of bacterial communities. As grazing intensified, the soil C and N content increased, as did the number and diversity of bacteria, mainly of fast-growing lineages. Aridibacter, Acidobacteria Gp6 and Gp10, Gemmatimonas, and Segetibacter increased their abundance along the grazing-intensity gradient. Firmicutes such as Romboutsia and Turicibacter from livestock microbiome also increased. In functional terms, the KEGG pathways enriched in the soils with moderate and high grazing intensity were ABC transporters, DNA repair and recombination proteins, the two-component system, and the degradation of xenobiotics. All of these proved to be related to stronger cell division and response mechanisms to environmental stressors such as drought, warming, toxic substances, and nutrient deprivation. Consequently, the bacterial community was affected by grazing, but appeared to adapt and counteract the effects of a high grazing intensity. Therefore, a clearly detrimental effect of grazing was not detected in the bacterial community of the soils studied.

Drought and vegetation restoration lead to shifts in soil microbial diversity and co-occurrence networks in California coastal prairie

Abstract Background and aims Both drought and vegetation restoration can have dramatic effects on plant community composition, but how they influence soil microbial community diversity, structure, and co-occurrence networks remain less well known. Methods To better understand the regulatory mechanisms of drought and vegetation restoration on soil microorganisms, we planted 12 native species in precipitation manipulation experimental plots in an invaded coastal grassland in California, USA. We measured soil bacterial and fungal community composition by amplicon sequencing, and quantified plant species richness and coverage in the third experimental year. Results Our results showed that drought significantly altered soil bacterial diversity and composition; however, neither drought nor vegetation restoration had significant effects on fungal diversity and composition. The control plots had the most cooperative interactions (greatest number of correlations) among bacterial and/or fungal species, while drought plots yielded the most complex co-occurrence network with the highest modularity and clustering coefficient. Structural equation modeling revealed that plant species richness, net gains, and soil moisture played dominant roles in shaping bacterial community structure. Drought and bacterial community structure directly affected fungal community structure. Plant dominant species cover, common species cover, and bacterial diversity were the key drivers in regulating the microbial co-occurrence network complex. Conclusion We conclude that soil bacterial and fungal communities differ in their responses to abiotic and biotic environmental changes, which may weaken the interspecies interactions among soil microorganisms.

Differential effects of winter cold stress on soil bacterial communities, metabolites, and physicochemical properties in two varieties of Tetrastigma hemsleyanum Diels & Gilg in reclaimed land.

Tetrastigma hemsleyanum Diels & Gilg (TDG) has been recently planted in reclaimed lands in Zhejiang Province, China, to increase reclaimed land use. Winter cold stress seriously limits the growth and development of TDG and has become the bottleneck limiting the TDG planting industry. To investigate the defense mechanisms of TDG toward winter cold stress when grown on reclaimed land, a combined analysis of soil bacterial communities, metabolites, and physicochemical properties was conducted in this study. Significant differences were observed in the composition of soil bacterial communities, metabolites, and properties in soils of a cold-tolerant variety (A201201) compared with a cold-intolerant variety (B201810). The fresh weight (75.8% of tubers) and dry weight (73.6%) of A201201 were significantly higher than those of B201810. The 16S rRNA gene amplicon sequencing of soil bacteria showed that Gp5 (25.3%), Gemmatimonas (19.6%), Subdivision3 (16.7%), Lacibacterium (11.9%), Gp4 (11.8%), Gp3 (10.4%), Gp6 (7.0%), and WPS-1 (1.2%) were less common, while Chryseolinea (10.6%) were more common in A201201 soils than B201810 soils. Furthermore, linear discriminant analysis of effect size identified 35 bacterial biomarker taxa for both treatments. Co-occurrence network analyses also showed that the structures of the bacterial communities were more complex and stable in A201201 soils compared to B201810 soils. In addition, ultra-high-performance liquid chromatography coupled to mass spectrometry analysis indicated the presence of significantly different metabolites in the two soil treatments, with 10 differentially expressed metabolites (DEMs) (8 significantly upregulated by 9.2%-391.3% and 2 significantly downregulated by 25.1%-73.4%) that belonged to lipids and lipid-like molecules, organic acids and derivatives, and benzenoids. The levels of those DEMs were significantly correlated with the relative abundances of nine bacterial genera. Also, redundancy discriminant analysis revealed that the main factors affecting changes in the bacterial community composition were available potassium (AK), microbial biomass nitrogen (MBN), microbial biomass carbon (MBC), alkaline hydrolysis nitrogen (AHN), total nitrogen (TN), available phosphorus (AP), and soil organic matter (SOM). The main factors affecting changes in the metabolite profiles were AK, MBC, MBN, AHN, pH, SOM, TN, and AP. Overall, this study provides new insights into the TDG defense mechanisms involved in winter cold stress responses when grown on reclaimed land and practical guidelines for achieving optimal TDG production.IMPORTANCEChina has been undergoing rapid urbanization, and land reclamation is regarded as a viable option to balance occupation and compensation. In general, the quality of reclaimed land cannot meet plant or even cultivation requirements due to poor soil fertility and high gravel content. However, Tetrastigma hemsleyanum Diels & Gilg (TDG), extensively used in Chinese herbal medicine, can grow well in stony soils with few nutrients. So, to increase reclaimed land use, TDG has been cultivated on reclaimed lands in Zhejiang Province, China, recently. However, the artificial cultivation of TDG is often limited by winter cold stress. The aim of this study was to find out how TDG on reclaimed land deal with winter cold stress by looking at the bacterial communities, metabolites, and physicochemical properties of the soil, thereby guiding production in practice.

Identification of bacteria and fungi responsible for litter decomposition in desert steppes via combined DNA stable isotope probing.

Soil microorganisms play crucial roles in determining the fate of litter in desert steppes because their activities constitute a major component of the global carbon (C) cycle. Human activities lead to increased ecosystem nitrogen (N) deposition, which has unpredictable impacts on soil microorganism diversity and functions. Nowadays, it is necessary to further study the succession of these microorganisms in the process of litter decomposition in desert steppe, and explore the effect of N deposition on this process. This issue is particularly important to resolve because it contributes to the broader understanding of nutrient cycling processes in desert steppes. In this study, DNA stable isotope probing (DNA-SIP) was used to study changes in soil bacterial and fungal community composition and function during 8 weeks of culture of 13C-labeled litter in desert steppes. The results were as follows: (1) Actinomycetota, Pseudomonadota, and Ascomycota are the main microorganisms involved in litter decomposition in desert steppes; (2) N deposition (50 kg ha-1 year-1) significantly increased the relative abundance of some microorganisms involved in the decomposition process; and (3) N deposition likely promotes litter decomposition in desert steppes by increasing the abundances of N cycles bacteria (usually carrying GH family functional genes). These findings contribute to a deeper understanding of the C assimilation mechanisms associated with litter residue production, emphasizing the importance of extensive C utilization.

The Impact of an Alien Snail Pomacea canaliculata Invading Coastal Saline Soils on Soil Chemical and Biological Properties

Recent studies have indicated that the invasive apple snail (Pomacea canaliculata) exhibits tolerance to the salinity levels present in coastal agricultural soils, suggesting that apple snails could potentially invade salt-affected coastal agricultural areas. However, the effects of the alien snail Pomacea canaliculata invasion on coastal saline soils, such as in terms of soil properties, microbial diversity, and abundance, remain poorly understood. To fill this gap, we conducted experiments involving three salinity levels (0, 2‰, and 5‰, w/w), coupled with varying snail densities (0, 5, and 10 snails per box), applied to agricultural soil. We analyzed soil chemical properties, enzyme activities, and bacterial communities. The findings revealed that heightened soil salinity increased soil electrical conductivity (EC) (exceeding 1312.67 μS cm−1). Under saline conditions, snail treatments significantly increased the soil organic matter (SOM) content from 15.82 mg kg−1 to 18.69 mg kg−1, and concurrently diminished the dissolved organic carbon (DOC) from 47.45 mg kg−1 to 34.60 mg kg−1. Both snail and salinity treatments resulted in ammonia nitrogen (NH4+-N) accumulation, while nitrate nitrogen (NO3−-N) concentrations remained low in salt-affected soils. A notable positive correlation existed between the EC and the activities of hydroxylamine reductase (HR) and peroxidase (POD), where HR exhibited a positive correlation with NH4+-N, and POD displayed a negative correlation with NO3−-N. Salinity substantially decreased the diversity and altered the composition of soil bacterial community, with the phyla Bacteroidota, Proteobacteria, and Firmicutes adapting to salt-affected soil environment and proliferating. Structural equation modeling (SEM) analysis indicated that snails exerted a direct influence on soil-available nitrogen (including NO3−-N and NH4+-N), while salinity impacted available nitrogen by modulating soil enzyme activities and bacterial communities. Our findings provide insights into how soil responds to the concurrent impacts of snail invasion and soil salinization, establishing some references for future research.

Variation of Soil Bacterial Communities in Forest Soil Contaminated with Chainsaw Lubricants.

Pollutants can exist in the soil for a long time and alter the bacterial community. Using lubricants to prevent the wear of chainsaw blades is necessary for thinning activities and wood harvesting. We investigated the influences of soil contamination with chainsaw lubricants on soil bacterial communities. Bio-oil, mineral oil, and recycled oil were scattered on each treatment to investigate variations in soil bacterial structure during treated periods using the Illumina MiSeq sequencing platform. The results obtained were 5943 ASVs, 5112 ASVs, and 6136 ASVs after treatment at one month, six months, and twelve months, respectively. There was a significant difference in Shannon and Simpson indices between treatments and controls. A total of 46 bacterial genera with an average relative abundance of more than 1.0% were detected in all soil samples. Massilia was the most common genus detected in control at one month, with an average relative abundance of 14.99%, while Chthoniobacter was the most abundant genus detected in bio-oil, mineral oil, and recycled oil treatments at one month, with an average relative abundance of 13.39%, 14.32%, and 10.47%, respectively. Among the three chainsaw lubricants, bio-oil and mineral oil had fewer impacts than recycled oil. The abundances of several functional bacteria groups in the bio-oil treatment were higher than in other treatments and controls. Our results indicated that different chainsaw lubricants and their time of application affected the soil bacterial community composition.

Effects of environmentally relevant concentrations of oxytetracycline and sulfadiazine on the bacterial communities, antibiotic resistance genes, and functional genes are different between maize rhizosphere and bulk soil.

Antibiotic contamination in soil has become a major concern worldwide. At present, it is not clear how two co-existed antibiotics with environmentally relevant concentrations would affect soil bacterial community structure, the abundances of antibiotic resistance genes (ARGs) and functional genes, and whether the effects of antibiotics would differ between rhizosphere and bulk soil. We conducted a greenhouse pot experiment to grow maize in a loess soil treated with oxytetracycline (OTC) or sulfadiazine (SDZ) or both at an environmentally relevant concentration (1 mg kg-1) to investigate the effects of OTC and SDZ on the rhizosphere and bulk soil bacterial communities, abundances of ARGs and carbon (C)-, nitrogen (N)-, and phosphorus (P)-cycling functional genes, and on plant growth and plant N and P nutrition. The results show that the effects of environmentally relevant concentrations of OTC and SDZ on bacterial communities and abundances of ARGs and functional genes differ between maize rhizosphere and bulk soil. The effects of two antibiotics resulted in a higher absolute abundances of accA, tet(34), tnpA-04, and sul2 in the rhizosphere soil than in the bulk soil and different bacterial community compositions and biomarkers in the rhizosphere soil and the bulk soil. However, OTC had a stronger inhibitory effect on the abundances of a few functional genes in the bulk soil than SDZ did, and their combination had no synergistic effect on plant growth, ARGs, and functional genes. The role of co-existed OTC and SDZ decreased shoot height and increased root N concentration. The results demonstrate that environmentally relevant concentrations of antibiotics shift soil microbial community structure, increase the abundances of ARGs, and reduce the abundances of functional genes. Furthermore, soil contamination with antibiotics can diminish agricultural production via phytotoxic effects on crops, and combined effects of antibiotics on plant growth and nutrient uptake should be considered.

Contrasting Altitudinal Patterns and Composition of Soil Bacterial Communities along Stand Types in Larix principis-rupprechtii Forests in Northern China

Bacterial communities inhabiting the soil of mountain ecosystems perform critical ecological functions. Although several studies have reported the altitudinal distribution patterns of bacterial communities in warm-temperate mountain forests, our understanding of typical zonal vegetation dominated by Larix principis-rupprechtii Mayr (abbreviated as larch hereafter) and the understory elevation distribution patterns of soil bacterial communities is still limited. In this study, the Illumina NovaSeq 6000 sequencing platform was used to investigate the changes of surface and subsurface soil bacterial communities along an altitudinal gradient (from 1720 m to 2250 m) in larch forests in northern China. Altitude significantly affected the relative abundance of Proteobacteria, Actinobacteria, Acidobacteria, and Chloroflexi (bacterial dominant phylum) and Alphaproteobacteria, Gammaproteobacteria, and Actinobacteria (bacterial dominant classes). The diversity of bacterial communities showed a concomitant increase with altitude. The variations in available nitrogen and soil temperature content at different altitudes were the main factors explaining the bacterial community structures in pure stands and mixed stands, respectively. Altitude and the contents of soil organic carbon and soil organic matter were the main factors explaining the dominant phylum (taxonomy). Our results suggest that stand type has a greater effect on the structure and composition of soil bacterial communities than elevation and soil depth, and bacterial communities show divergent patterns along the altitudes, stand types, and soil profiles.

Green Waste Compost Impacts Microbial Functions Related to Carbohydrate Use and Active Dispersal in Plant Pathogen-Infested Soil

The effects of compost on physical and chemical characteristics of soil are well-studied but impacts on soil microbiomes are poorly understood. This research tested effects of green waste compost on bacterial communities in soil infested with the plant pathogen Fusarium oxysporum. Compost was added to pathogen-infested soil and maintained in mesocosms in a greenhouse experiment and replicated growth chamber experiments. Bacteria and F. oxysporum abundance were quantified using quantitative PCR. Taxonomic and functional characteristics of bacterial communities were measured using shotgun metagenome sequencing. Compost significantly increased bacterial abundance 8 weeks after amendment in one experiment. Compost increased concentrations of chemical characteristics of soil, including phosphorus, potassium, organic matter, and pH. In all experiments, compost significantly reduced abundance of F. oxysporum and altered the taxonomic composition of soil bacterial communities. Sixteen bacterial genera were significantly increased from compost in every experiment, potentially playing a role in pathogen suppression. In all experiments, there was a consistent negative effect of compost on functions related to carbohydrate use and a positive effect on bacteria with flagella. Results from this work demonstrate that compost can reduce the abundance of soilborne plant pathogens and raise questions about the role of microbes in plant pathogen suppression.