Soil Bacteria Research Articles

Isolation and identification of the dominant bacteria from the soil contaminated with hydrocarbon

The aim of this research to isolate and determine the most dominant bacteria in soil contaminated by hydrocarbons. Commercial, industrial, and military activity, largely in the 19th and 20th centuries, have led to environmental pollution that can threaten human health and ecosystem function are the major sources of energy for industry and daily life that cause environmental contamination during various stages of production, transportation, refining and use. Four samples of contaminated soil were collected from Al-Amriya Gas Filling Factory in November, 2023 sampling of depth (0-15 cm) then all samples transported to the laboratory. Results revealed that dominant isolates are Kocuria rosea, Escherichia coli, and Pseudomonas aeruginosa. These isolates identified depending on morphological cultural, gram stain, microscopic features, biochemical tests, and VITEK2 compact

Membrane-based preparation for mass spectrometry imaging of cultures of bacteria.

The study of the dialogue between microorganisms at the molecular level is becoming essential to understand their relationship (antagonist, neutral, or beneficial interactions) and its impact on the organization of the microbial community. Mass spectrometry imaging (MSI) with matrix-assisted laser desorption/ionization (MALDI) is a technique that reveals the spatial distribution of molecules on a sample surface that may be involved in interactions between organisms. An experimental limitation to perform MALDI MSI is a flat sample surface, which in many cases could not be achieved for bacterial colonies such as filamentous bacteria (e.g., Streptomyces). In addition, sample heterogeneity affects sample dryness and MALDI matrix deposition prior to MSI. To avoid such problems, we introduce an additional step in the sample preparation. A polymeric membrane is interposed between the microorganisms and the agar-based culture medium, allowing the removal of bacterial colonies prior to MSI of the homogeneous culture medium. A proof of concept was evaluated on Streptomyces ambofaciens (a soil bacterium) cultures on solid media. As the mycelium was removed at the same time as the polymeric membrane, the metabolites released into the medium were spatially resolved by MALDI MSI. In addition, extraction of the recovered mycelium from the membrane confirmed the identification of the metabolites by ESI MS/MS analysis. This approach allows both the spatial distribution of metabolites produced by microorganisms in an agar medium to be studied under well-controlled sample preparation and their structure to be elucidated. This capability is illustrated using desferrioxamine E, a siderophore produced by S. ambofaciens.

Isolation of Massilia species capable of degrading Poly(3-hydroxybutyrate) isolated from eggplant (Solanum melongena L.) field

Poly(3-hydroxybutyrate) (PHB) is crucial for replacing petroleum-based plastics, an essential step towards fostering a bio-based economy. This shift is urgently needed to safeguard human health and preserve natural ecosystems. PHB is one of the most extremely commercialized bio-plastics. Although.significant progress has been made in identifying bacteria that produce PHB, fewer bacteria capable of degrading it have been discovered. Four newly isolated Massilia strains capable of degrading PHB were discovered in eggplant (Solanum melongena L.) field soil. Their PHB-degrading abilities were investigated under different temperatures and media using emulsified solid-media based cultures. The strains belong to the genus Massilia, were evaluated for their effectiveness. Among them, Massilia sp. JJY02, was selected for its exceptional PHB degradation. PHB degradation was confirmed by monitoring changes in the physical and chemical properties of PHB films using scanning electron microscopy (SEM), Fourier-transform infrared spectroscopy (FTIR) and gel permeation chromatography (GPC). After 20 days of cultivation with PHB film, Massilia sp. JJY02 achieved approximately 90% PHB degradation at 28 °C. All the novel strains were capable of producing carotenoid-type pigments and indole-acetic acid (IAA). Among them, Massilia sp. JJY03 and JJY04 showed phosphate solubilization activity. This study demonstrated that soil bacteria from eggplant have both PHB-degrading and plant growth promoting capabilities, marking the first instance of showing that species of Massilia can degrade PHB.

Impact of organic carbon composition on bacterial taxa assembly upon phosphorus addition in organic and mineral soil layers of a Robinia pseudoaccacia plantation

Increasing phosphorus (P) inputs significantly affect the nutrient cycle of terrestrial ecosystems. The community structure and assembly processes of soil bacteria, which are the primary participants in nutrient cycling within terrestrial ecosystems, are affected by P inputs. However, the assembly processes and driving mechanisms of soil bacterial communities in artificial forest ecosystems in response to P inputs remain unclear. Therefore, in this study, we conducted in situ experimental P additions (0, 0.5, 1, 2, and 4 g P m-2 year-1) to artificial Robinia pseudoacacia forests on the Loess Plateau. We investigated the effects of P addition on the soil organic carbon (SOC) composition, bacterial community characteristics (total, abundant, and rare taxa), and assembly processes in the organic horizon (OH) and mineral horizon (MH) layers of the soil. The results showed that P addition significantly changed soil physicochemical factors, such as available P (AP), SOC content, and SOC composition in terms of the labile (LC) and recalcitrant carbon (RC) fractions. The proportion of the LC fraction increased in OH and decreased in MH, whereas the RC fraction showed the opposite trends. P addition increased the proportion of eutrophic bacteria in OH, whereas it decreased the proportion of oligotrophic bacteria. In contrast to those in OH, the changes in eutrophic and oligotrophic bacteria in MH exhibited the opposite trend. With increasing P levels, the diversity of the bacterial communities in the OH did not change significantly. In the MH, total and rare taxa diversity increased, while the diversity of abundant taxa decreased. During P addition, the total and rare taxa bacterial communities showed stochastic assembly, whereas the assembly of abundant taxa shifted from stochastic to deterministic processes in the OH and from deterministic to stochastic processes in the MH. The structural equation model revealed that during P addition, the assembly of total and rare bacterial communities in the OH and MH was regulated by AP and the LC fraction, respectively. Meanwhile, the assembly of abundant taxa in OH and MH was influenced by the LC fraction and RC fraction, respectively. Our findings highlight the critical role of SOC composition across different bacterial taxa, with abundant bacterial taxa exhibiting heightened sensitivity to environmental filtration and the availability of SOC resources. Our study provides new insights into the community assembly and driving mechanisms of soil bacteria in artificial forest soils during P addition.

Impact of a Single Lignite Humic Acid Application on Soil Properties and Microbial Dynamics in Aeolian Sandy Soils: A Fourth-Year Study in Semi-Arid Inner Mongolia

Humic acid (HA) is considered a promising soil amendment for improving soil fertility. However, the effects of HA application on the microbial community, especially in aeolian sandy soils of semi-arid regions, remain insufficiently elucidated. To address this gap, a field experiment was conducted to investigate the changes in soil properties, bacterial and fungal diversity, and community structure in a buckwheat field in the fourth year after a single application of lignite humic acid (L-HA) at 0 (L-HA0), 2 (L-HA1), 4 (L-HA2), and 6 (L-HA3) ton·ha−1 in an aeolian sandy soil in Inner Mongolia, China. The results demonstrated that four years after L-HA application, there was a significant (p < 0.05) decrease in soil pH, accompanied by an increase in soil water content and nutrient levels, including organic matter and total N, available P, and K. Additionally, the application of L-HA enhanced microbial biomass C and N and stimulated enzyme activities, such as urease and invertase, with these effects being more pronounced at higher application rates (L-HA2 and L-HA3). However, HA addition did not significantly (p < 0.05) affect soil microbial biomass P or alkaline phosphatase activity. The L-HA amendment enhanced the α-diversity indices of soil bacteria but did not significantly (p < 0.05) affect soil fungal diversity. The addition of L-HA induced significant changes in the composition of the soil microbial community at both the phylum and genus levels, with significant variability in microbial responses observed across the different L-HA application rates. The incorporation of L-HA notably enriched the composition of bacterial and fungal communities at the phylum level, particularly those involved in carbon cycling, including the bacterial phyla Proteobacteria and Actinobacteriota and the fungal phyla Ascomycota and Rozellomycota. At the genus level, higher L-HA application rates, specifically L-HA2 and L-HA3, exerted statistically significant (p < 0.05) effects on most bacterial and fungal genera. Specifically, these treatments increased the abundance of bacterial genera, such as Rokubacterium and fungal genera, including Plectosphaerella, Tausonia, Talaromyces, and Clonostachys. Conversely, the relative abundance of the bacterial genera Vicinamibacter and Subgroup_7, as well as the fungal genus Niesslia, was significantly reduced. Redundancy analysis (RDA) indicated that bacterial community compositions were closely associated with soil parameters, such as available P (AP), microbial biomass carbon (SMC), microbial biomass nitrogen (SMN), microbial biomass phosphorus (SMP), and invertase, while all tested soil parameters, except for alkaline phosphatase, significantly influenced the fungal community structure. Given that the changes in these soil parameters were highly correlated with the amounts of L-HA addition, this suggests that the impacts of long-term L-HA amendment on the soil bacterial and fungal communities were linked to alterations in soil physicochemical and biological properties.

Determination of the Effects of Pear-Morchella Intercropping Mode on M. sextelata Quality, Yield, and Soil Microbial Community.

The intercropping of Morchella in pear orchards has important production value in improving the utilization rate and economic benefits of the orchard; however, there is little research on the intercropping model of pear-Morchella. In this study, metabolomics analysis found that compared with greenhouse cultivation, there were 104 and 142 metabolites significantly increased and decreased in the intercropping mode of M. sextelata, respectively. Among them, there was a significant accumulation of amino acids (phenylalanine, lysine, proline, citrulline, and ornithine), sugars (arabinitol and glucosamine), and organic acids (quinic acid, fumaric acid, and malic acid) related to the unique taste of Morchella in intercropping cultivation. In addition, research on the cultivation model using exogenous nutrient bags indicated that placing the density of six exogenous nutrient bags per square meter was most suitable for yield formation. Adding pear sawdust to the nutrient bags (PN) significantly increased the yield of morel per unit area. Moreover, soil microbial community analysis showed that fungal alpha diversity dramatically declined in PN-cultivated soil, which decreased the relative abundance of soil-borne fungal pathogens, including Fusarium and Aspergillus. Some beneficial soil bacteria abundance increased in the PN-used soil, such as Pedobacter, Pseudomonas, and Devosia. This study provides novel insights into the effects of intercropping on the internal quality of Morchella and enriches the theoretical knowledge on the consummation of the pear-Morchella model formation, further improving agricultural resource utilization efficiency and crop productivity.

Nitrogen enrichment stimulates nutrient cycling genes of rhizosphere soil bacteria in the Phoebe bournei young plantations

Anthropogenic nitrogen (N) deposition is expected to increase substantially and continuously in terrestrial ecosystems, endangering the balance of N and phosphorus (P) in P-deficient subtropical forest soil. Despite the widely reported responses of the microbial community to simulated N deposition, there is limited understanding of how N deposition affects the rhizosphere soil processes by mediating functional genes and community compositions of soil bacteria. Here, five levels of simulated N deposition treatments (N0, 0 g m−2·yr−1; N1, 100 g m−2·yr−1; N2, 200 g m−2·yr−1; N3, 300 g m−2·yr−1; and N4, 400 g m−2·yr−1) were performed in a 10-year-old Phoebe bournei plantation. Quantitative microbial element cycling smart chip technology and 16S rRNA gene sequencing were employed to analyze functional gene compositions involved in carbon (C), N, and P cycling, as well as rhizosphere bacterial community composition. N deposition significantly influenced C cycling relative abundance of genes in the rhizosphere soil, especially those involved in C degradation. Low and moderate levels (100–300 g m−2·yr−1) of N deposition promoted the relative abundance of the C decomposition-related genes (e.g., amyA, abfA, pgu, chiA, cex, cdh, and glx), whereas high N deposition (400 g m−2·yr−1) suppressed enzyme (e.g., soil invertase, soil urease, and soil acid phosphatase) activities, affecting the C cycling processes in the rhizosphere. Simulated N deposition affected the functional genes associated with C, N, and P cycling by mediating soil pH and macronutrients. These findings provide new insights into the management of soil C sequestration in P. bournei young plantations as well as the regulation of C, N, and P cycling and microbial functions within ecosystems.

Impacts of soil type on the temporal dynamics of antibiotic resistance gene profiles following application of composted manure

Farmland application of composted manure is associated with a risk of dissemination of antibiotic resistance genes (ARGs) in agricultural soils. However, the impact of soil type on the temporal dynamics of ARGs in agricultural soil remains largely unclear. The aims of this study were to study the persistence of composted manure-derived ARGs in six soil types representative for Chinese agriculture and to explore the underlying environmental drivers of soil ARG profiles in a controlled greenhouse experiment. Temporal dynamics of manure-derived ARGs was strongly affected by soil type. High persistence of fertilizer-derived ARGs was evident in red soil, yellow soil and sierozem soil, while a rapid decrease to near pre-fertilization levels (low persistence) was observed in yellow-brown soil, black soil and brown earth soil. The distribution of ARGs was linked to soil properties such as soil texture, pH and concentrations of heavy metals. More complex co-occurrence networks of ARGs and bacteria in red soil, yellow soil, and sierozem soil suggested a higher dissemination potential, which was consistent with the significantly increased abundance of MGEs in these three types of soils. Our findings highlight the necessity for developing tailored fertilization strategies for different soil types to mitigate environmental dissemination of ARGs.

Isolation, Antibacterial Activity and Molecular Identification of Avocado Rhizosphere Actinobacteria as Potential Biocontrol Agents of Xanthomonas sp.

Actinobacteria, especially the genus Streptomyces, have been shown to be potential biocontrol agents for phytopathogenic bacteria. Bacteria spot disease caused by Xanthomonas spp. may severely affect chili pepper (Capsicum annuum) crops with a subsequent decrease in productivity. Therefore, the objective of the study was to isolate rhizospheric actinobacteria from soil samples treated by physical methods and evaluate the inhibitory activity of the isolates over Xanthomonas. Initially, soil samples collected from avocado tree orchards were treated by dry heat air and microwave irradiation; thereafter, isolation was implemented. Then, antibacterial activity (AA) of isolates was evaluated by the double-layer agar method. Furthermore, the positive/negative effect on AA for selected isolates was evaluated on three culture media (potato-dextrose agar, PDA; yeast malt extract agar, YME; and oat agar, OA). Isolates were identified by 16S rRNA sequence analysis. A total of 198 isolates were obtained; 76 (series BVEZ) correspond to samples treated by dry heat and 122 strains (series BVEZMW) were isolated from samples irradiated with microwaves. A total of 19 dry heat and 25 microwave-irradiated isolates showed AA with inhibition zones (IZ, diameter in mm) ranging from 12.7 to 82.3 mm and from 11.4 to 55.4 mm, respectively. An increment for the AA was registered for isolates cultured on PDA and YME, with an IZ from 21.1 to 80.2 mm and 14.1 to 69.6 mm, respectively. A lower AA was detected when isolates were cultured on OA media (15.0 to 38.1 mm). Based on the 16S rRNA gene sequencing analysis, the actinobacteria belong to the Streptomyces (6) and Amycolatopsis (2) genera. Therefore, the study showed that microwave irradiation is a suitable method to increase the isolation of soil bacteria with AA against Xanthomonas sp. In addition, Streptomyces sp. BVEZ 50 was the isolate with the highest IZ (80.2 mm).

Unprecedented N2O production by nitrate-ammonifying Geobacteraceae with distinctive N2O isotopocule signatures.

Dissimilatory nitrate reduction to ammonium (DNRA), driven by nitrate-ammonifying bacteria, is an increasingly appreciated nitrogen-cycling pathway in terrestrial ecosystems. This process reportedly generates nitrous oxide (N2O), a strong greenhouse gas with ozone-depleting effects. However, it remains poorly understood how N2O is produced by environmental nitrate-ammonifiers and how to identify DNRA-derived N2O. In this study, we characterize two novel enzymatic pathways responsible for N2O production in Geobacteraceae strains, which are predominant nitrate-ammonifying bacteria in paddy soils. The first pathway involves a membrane-bound nitrate reductase (Nar) and a hybrid cluster protein complex (Hcp-Hcr) that catalyzes the conversion of NO2- to NO and subsequently to N2O. The second pathway is observed in Nar-deficient bacteria, where the nitrite reductase (NrfA) generates NO, which is then reduced to N2O by Hcp-Hcr. These enzyme combinations are prevalent across the domain Bacteria. Moreover, we observe distinctive isotopocule signatures of DNRA-derived N2O from other established N2O production pathways, especially through the highest 15N-site preference (SP) values (43.0‰-49.9‰) reported so far, indicating a robust means for N2O source partitioning. Our findings demonstrate two novel N2O production pathways in DNRA that can be isotopically distinguished from other pathways.IMPORTANCEStimulation of DNRA is a promising strategy to improve fertilizer efficiency and reduce N2O emission in agriculture soils. This process converts water-leachable NO3- and NO2- into soil-adsorbable NH4+, thereby alleviating nitrogen loss and N2O emission resulting from denitrification. However, several studies have noted that DNRA can also be a source of N2O, contributing to global warming. This contribution is often masked by other N2O generation processes, leading to a limited understanding of DNRA as an N2O source. Our study reveals two widespread yet overlooked N2O production pathways in Geobacteraceae, the predominant DNRA bacteria in paddy soils, along with their distinctive isotopocule signatures. These findings offer novel insights into the role of the DNRA bacteria in N2O production and underscore the significance of N2O isotopocule signatures in microbial N2O source tracking.

Roles of straw return in shaping denitrifying bacteria in rice rhizosphere soils through effects on root exudates and soil metabolites

Roles of straw return in shaping denitrifying bacteria in rice rhizosphere soils through effects on root exudates and soil metabolites

The role of microbiomes in cooperative detoxification mechanisms of arsenate reduction and arsenic methylation in surface agricultural soil.

Microbial arsenic (As) transformations play a vital role in both driving the global arsenic biogeochemical cycle and determining the mobility and toxicity of arsenic in soils. Due to the complexity of soils, variations in soil characteristics, and the presence and condition of overlying vegetation, soil microbiomes and their functional pathways vary from site to site. Consequently, key arsenic-transforming mechanisms in soil are not well characterized. This study utilized a combination of high-throughput amplicon sequencing and shotgun metagenomics to identify arsenic-transforming pathways in surface agricultural soils. The temporal and successional variations of the soil microbiome and arsenic-transforming bacteria in agricultural soils were examined during tropical monsoonal dry and wet seasons, with a six-month interval. Soil microbiomes of both dry and wet seasons were relatively consistent, particularly the relative abundance of Chloroflexi, Gemmatimonadota, and Bacteroidota. Common bacterial taxa present at high abundance, and potentially capable of arsenic transformations, were Bacillus, Streptomyces, and Microvirga. The resulting shotgun metagenome indicated that among the four key arsenic-functional genes, the arsC gene exhibited the highest relative abundance, followed by the arsM, aioA, and arrA genes, in declining sequence. Gene sequencing data based on 16S rRNA predicted only the arsC and aioA genes. Overall, this study proposed that a cooperative mechanism involving detoxification through arsenate reduction and arsenic methylation was a key arsenic transformation in surface agricultural soils with low arsenic concentration (7.60 to 10.28 mg/kg). This study significantly advances our knowledge of arsenic-transforming mechanisms interconnected with microbial communities in agricultural soil, enhancing pollution control measures, mitigating risks, and promoting sustainable soil management practices.

Forest types matter for the community and co-occurrence network patterns of soil bacteria, fungi, and nematodes

Tree growth influences the biological, physical, and chemical properties of the soil through the input of different types of litter and various root exudates. However, our understanding of tree-mediated effects on the composition and diversity of soil biota remains limited. This study aimed to determine the effects of physically neighboring forest types (i.e., an artificial Japanese cedar (Cryptomeria japonica) plantation vs. a broadleaf (Quercus serrata) secondary forest) on individual bacterial, fungal, and nematode communities and the associations among these inter-kingdoms. Bacterial, fungal, and nematode aggregates were estimated using MiSeq high-throughput sequencing system. The amplicon sequence variant richness of fungi and nematodes was significantly greater in the cedar plantation than in the broadleaf forest, and the three soil biota community structures were significantly clustered among the forest types. Environmental factors such as soil pH, C, N, and C/N ratio significantly influenced the three soil biota community structures. The bacterial–fungal–nematode co-occurrence network of the broadleaf forest had more nodes and edges than that of the cedar plantation. Moreover, Ascomycota and Basidiomycota fungi mainly co-occurred with fungivorous nematodes in the cedar and broadleaf forests, respectively. Our results suggested that unique soil biota communities and characteristic co-occurrence network patterns were established among the tripartite inter-kingdom relationships between adjacent forest types.

Unraveling the key mechanisms of Gastrodia elata continuous cropping obstacles: soil bacteria Massilia, Burkholderia-Caballeronia-Paraburkholderia, and Dyella along with soil metabolites 4-hydroxy-benzenemethanol and N-(2-butyl)-N-octadecyl-, ethyl ester as crucial indicators.

Tian-ma (Gastrodia elata) is a traditional medicinal herb found in China. It is used in healthy food and to treat various diseases, therefore cultivated extensively in southwest China. However, continuous cropping of this species has led to various obstacles, such as microbial disease and pest infestation, significantly affecting the production and development of valuable medicinal and food resources. As per the growth habit, soil is presumed to be the primary factor contributing to these obstacles, despite the known issues of continuous cropping obstacles in Gastrodia elata, such as microbial disease, there is a lack of comprehensive understanding of the specific soil bacterial communities and metabolites involved in these processes. We analyzed soil samples collected during the year of Tian-ma cultivation (0 Year), after the Tian-ma harvest (1 Year), after two years (2 Year), and three years (3 Year) of fallowing post-cultivation using soil 16S rRNA metabarcoding sequencing by illumina platform and metabolomics (GC-MS/MS). Soil sample collected from the uncultivated field was used as the control (CK). Metabarcoding sequencing showed high bacterial alpha diversity during the cultivation of Tian-ma (0 Year) and the period of deterioration of soil bacterial community. (1 Year), with decreased anaerobic bacterial abundance and increased copiotrophic bacterial abundance. Bacteria associated with sulfur metabolism also showed increased abundance during the year of cropping obstacles. Further metabolomics approach identified 4-hydroxy-benzenemethanol as an indicator of Tian-ma continuous cropping obstacles. Besides, metabolites of the carbohydrate class were found to be the most abundant during the occurrence of continuous cropping obstacles of Gastrodia elata, suggesting that regulation of soil microbial diversity may be a critical factor in addressing these obstacles. Finally, the correlation analysis indicated a positive association between the abundance of some metabolite, e.g., carbamic acid, N-(2-butyl)-N-octadecyl-, ethyl ester detected after Tian-ma cultivation and the abundance of bacteria capable of degrading toxic metabolites, such as Massilia, Burkholderia-Caballeronia-Paraburkholderia, and Dyella. This study has revealed the specific soil bacteria and metabolic factors related to the continuous cropping obstacles of Gastrodia elata. These findings not only deepen our understanding of the continuous cropping issues but also pave the way for developing effective strategies to overcome them.

Isolation of Heavy Metal-Tolerant and Anti-Phytopathogenic Plant Growth-Promoting Bacteria from Soils.

In this study, multifunctional soil bacteria, which can promote plant development, resist heavy metals, exhibit anti-phytopathogenic action against plant diseaes, and produce extracellular enzymes, were isolated to improve the effectiveness of phytoremediation techniques. In order to isolate multifunctional soil bacteria, a variety of soil samples with diverse characteristics were used as sources for isolation. To look into the diversity and structural traits of the bacterial communities, we conducted amplicon sequencing of the 16S rRNA gene on five types of soils and predicted functional genes using Tax4Fun2. The isolated bacteria were evaluated for their multifunctional capabilities, including heavy metal tolerance, plant growth promotion, anti-phytopathogenic activity, and extracellular enzyme activity. The genes related to plant growth promotion and anti-phytopathogenic activity were most abundant in forest and paddy soils. Burkholderia sp. FZ3 and FZ5 demonstrated excellent heavy metal resistance (≤ 1 mM Cd and ≤ 10 mM Zn), Pantoea sp. FC24 exhibited the highest protease activity (24.90 μmol tyrosine·g-DCW-1·h-1), and Enterobacter sp. PC20 showed superior plant growth promotion, especially in siderophore production. The multifunctional bacteria isolated using traditional methods included three strains (FC24, FZ3, and FZ5) from the forest and one strain (PC20) from paddy field soil. These results indicate that, for the isolation of beneficial soil microorganisms, utilizing target gene information obtained from isolation sources and subsequently exploring target microorganisms is a valuable strategy.

Soil bacterial community characteristics and influencing factors in different types of farmland shelterbelts in the Alaer reclamation area.

To investigate the effects of various types of farmland shelterbelts on soil quality and soil bacterial community diversity, this study focused on soil samples from four different shelterbelt types in the Alaer reclamation area, including Populus euphratica Oliv.- Populus tomentosa Carrière (PP), Elaeagnus angustifolia L.- Populus euphratica Oliv. (EP), Populus alba var. pyramidalis Bunge (P), and Salix babylonica L. (S). We analyzed their physical, chemical, biological properties as well as the differences in bacterial community structure, and explored the influencing factors on soil microbial community characteristics through microbial correlation network analysis. The results showed that: (1) There were significant differences in soil properties among the four types of farmland shelterbelts (p < 0.05), with P soils exhibiting the highest levels of organic matter, total nitrogen, and total phosphorus contents. (2) The Alpha diversity indices of soil bacteria showed significant differences among the four types of farmland shelterbelts (p < 0.05), with the P soils displayed the highest Chao1 and Shannon indices. (3) There were differences in the composition and abundance of dominant soil bacterial communities among different farmland shelterbelts, notably, the abundances of Verrucomicrobia, Acidobacteria, and Planctomycetes were significantly higher in P soils compared to the other three types. (4) The complexity of the correlation network between microbial species and environmental factors was highest in EP soils, soil microbial biomass nitrogen and available phosphorus were the main influencing factors. These findings indicated that different types of farmland shelterbelts had significant impacts on soil properties and soil bacterial communities. Soil bacterial communities were regulated by soil properties, their changes reflected a combined effect of soil characteristics and tree species.

Understanding the Crucial Role of Phosphate and Iron Availability in Regulating Root Nodule Symbiosis.

The symbiosis between legumes and nitrogen-fixing bacteria (rhizobia) is instrumental in sustaining the nitrogen cycle and providing fixed nitrogen to the food chain. Both partners must maintain an efficient nutrient exchange to ensure a successful symbiosis. This mini-review highlights the intricate phosphate and iron uptake and homeostasis processes taking place in legumes during their interactions with rhizobia. The coordination of transport and homeostasis of these nutrients in host plants and rhizobia ensures an efficient nitrogen fixation process and nutrient use. We discuss the genetic machinery controlling the uptake and homeostasis of these nutrients in the absence of rhizobia and under symbiotic conditions with this soil bacterium. We also highlight the genetic impact of the availability of phosphate and iron to coordinate the activation of the genetic programs that allow legumes to engage in symbiosis with rhizobia. Finally, we discuss how the transcription factor phosphate starvation response might be a crucial genetic element to integrate the plant's needs of nitrogen, iron and phosphate while interacting with rhizobia. Understanding the coordination of the iron and phosphate uptake and homeostasis can lead us to better harness the ecological benefits of the legume-rhizobia symbiosis, even under adverse environmental conditions.

Soil microbial community composition by crop type under rotation diversification

BackgroundCrop rotation is an important agricultural practice that often affects the metabolic processes of soil microorganisms through the composition and combination of crops, thereby altering nutrient cycling and supply to the soil. Although the benefits of crop rotation have been extensively discussed, the effects and mechanisms of different crop combinations on the soil microbial community structure in specific environments still need to be analyzed in detail.Materials and methodsIn this study, six crop rotation systems were selected, for which the spring crops were mainly tobacco or gramineous crops: AT (asparagus lettuce and tobacco rotation), BT (broad bean and tobacco rotation), OT (oilseed rape and tobacco rotation), AM (asparagus lettuce and maize rotation), BM (broad bean and maize rotation), and OR (oilseed rape and rice rotation). All crops had been cultivated for > 10 years. Soil samples were collected when the rotation was completed in spring, after which the soil properties, composition, and functions of bacterial and fungal communities were analyzed.ResultsThe results indicate that spring cultivated crops play a more dominant role in the crop rotation systems than do autumn cultivated crops. Crop rotation systems with the same spring crops have similar soil properties and microbial community compositions. pH and AK are the most important factors driving microbial community changes, and bacteria are more sensitive to environmental responses than fungi. Rotation using tobacco systems led to soil acidification and a decrease in microbial diversity, while the number of biomarkers and taxonomic indicator species differed between rotation patterns. Symbiotic network analysis revealed that the network complexity of OT and BM was the highest, and that the network density of tobacco systems was lower than that of gramineous systems.ConclusionsDifferent crop rotation combinations influence both soil microbial communities and soil nutrient conditions. The spring crops in the crop rotation systems had stronger dominating effects, and the soil bacteria were more sensitive than the fungi were to environmental changes. The tobacco rotation system can cause soil acidification and thereby affect soil sustainability, while the complexity of soil microbial networks is lower than that of gramineous systems. These results provide a reference for future sustainable applications of rotation crop systems.

Longitudinal distributions of CO2-fixing bacteria in forest soils and their potential associations with soil multifunctionality

Autotrophic microorganisms can fix carbon dioxide (CO2) into organic carbon (C), potentially offering a natural mechanism to mitigate global climate change. Forest soils, recognized as vast and critical C repositories with significant microbial CO2 fixation rates, remain understudied, particularly regarding the spatial variations of autotrophic bacteria and their relationship to soil functions in arid regions. In this study, we systematically investigated soil multifunctionality, along with the spatial distribution of autotrophic bacterial communities identified by the RubisCO cbbL and cbbM genes, and the driving factors across a longitudinal gradient in the Loess Plateau forest soils. The investigation spanned an ∼850 km west-east transect with precipitation below 600 mm. The alpha diversity of cbbL-containing bacteria, as measured by the Chao1 index, was correlated with climatic variables such as precipitation and elevation instead of local soil characteristics. In contrast, the alpha diversity of cbbM-containing bacteria was associated with soil properties. The community composition of autotrophic bacteria, based on cbbL and cbbM genes, showed greater similarity in soils from the eastern Loess Plateau and was distinct from those in the western region. The cbbL- and cbbM-containing generalist taxa were subject to differential selection and promotion between the eastern and western regions. Temperature, soil pH and spatial variables were key drivers influencing the community composition of cbbL- and cbbM-containing bacteria. The diversity and communities of soil autotrophic bacteria significantly affected soil multifunctionality. The study demonstrates that soil autotrophic bacteria in forest soils are intricately connected to climatic conditions, soil pH and spatial factors, significantly impacting soil multifunctionality. These insights provide evidence that can be instrumental in predicting and potentially enhancing the functional capacity of forest ecosystems in the Loess Plateau.

Transcriptomic analyses of bacterial growth on fungal necromass reveal different microbial community niches during degradation.

Bacteria are major drivers of organic matter decomposition and play crucial roles in global nutrient cycling. Although the degradation of dead fungal biomass (necromass) is increasingly recognized as an important contributor to soil carbon (C) and nitrogen (N) cycling, the genes and metabolic pathways involved in necromass degradation are less characterized. In particular, how bacteria degrade necromass containing different quantities of melanin, which largely control rates of necromass decomposition in situ, is largely unknown. To address this gap, we conducted a multi-timepoint transcriptomic analysis using three Gram-negative, bacterial species grown on low or high melanin necromass of Hyaloscypha bicolor. The bacterial species, Cellvibrio japonicus, Chitinophaga pinensis, and Serratia marcescens, belong to genera known to degrade necromass in situ. We found that while bacterial growth was consistently higher on low than high melanin necromass, the CAZyme-encoding gene expression response of the three species was similar between the two necromass types. Interestingly, this trend was not shared for genes encoding nitrogen utilization, which varied in C. pinensis and S. marcescens during growth on high vs low melanin necromass. Additionally, this study tested the metabolic capabilities of these bacterial species to grow on a diversity of C and N sources and found that the three bacteria have substantially different utilization patterns. Collectively, our data suggest that as necromass changes chemically over the course of degradation, certain bacterial species are favored based on their differential metabolic capacities.IMPORTANCEFungal necromass is a major component of the carbon (C) in soils as well as an important source of nitrogen (N) for plant and microbial growth. Bacteria associated with necromass represent a distinct subset of the soil microbiome and characterizing their functional capacities is the critical next step toward understanding how they influence necromass turnover. This is particularly important for necromass varying in melanin content, which has been observed to control the rate of necromass decomposition across a variety of ecosystems. Here we assessed the gene expression of three necromass-degrading bacteria grown on low or high melanin necromass and characterized their metabolic capacities to grow on different C and N substrates. These transcriptomic and metabolic studies provide the first steps toward assessing the physiological relevance of up-regulated CAZyme-encoding genes in necromass decomposition and provide foundational data for generating a predictive model of the molecular mechanisms underpinning necromass decomposition by soil bacteria.