Bacterial diversity and composition in major fresh produce growing soils affected by physiochemical properties and geographic locations

Variations in soil microbial communities in different saline soils under typical Populus spp. vegetation in alpine region of the Qaidam Basin, NW China

Salinization is a severe threat to agriculture and the environment in many areas, and the same in Qaidam Basin, Qinghai Province, Northwestern China. Microorganisms have an important influence on regulating the biochemical cycles of ecosystems; however, systematic research exploring microbial diversity and interactions with saline-soil ecosystems' environmental variables remains scarce. Thus, 16 S rRNA high-throughput sequencing was performed in this paper to characterize microbial diversity under different levels of salinized soils: non-salinized (NS, 2.25 g/L), moderately salinized (MS, 6.14 g/L) and highly salinized (HS, 9.82 g/L). The alpha diversity results showed that the HS soil was significantly different from the NS and MS soils. An analysis of similarity (ANOSIM) and a principal co-ordinates analysis (PCoA) indicated that NS and MS clustered closely while HS separated from the other two. Significant differences in microbial composition were observed at the taxonomic level. Proteobacteria (42.29-79.23 %) were the most abundant phyla in the studied soils. Gammaproteobacteria (52.49 and 66.61 %) had higher abundance in the MS and HS soils at the class level; Methylophaga and Pseudomonas were the predominant bacteria in the HS soil; and Azotobacter and Methylobacillus were abundant in the MS soil. Most genera belonging to Proteobacteria and Actinobacteria were detected via a linear discriminate analysis (LDA) effect size (LEfSe) analysis, which indicated that microbes with the ability to degrade organic matter and accomplish nutrient cycling can be well-adapted to salt conditions. Further analyses (redundancy analysis and Mantel test) showed that the microbial communities were mainly related to the soil salinity, electrical conductivity (EC1:5), total phosphorus (TP) and ammonia nitrogen (NH4+-N). Overall, the findings of the study can provide insights for better understanding the dominant indigenous microbes and their roles in biochemical cycles in different saline soils in the Qaidam Basin, Qinghai Province, China. The researches related to microbial community under typical poplar species should further clarify the mechanism of plant-microbial interaction and benefit for microbial utilization in salt soil remediation.

Variation in Bacterial and Fungal Communities in Soils from Three Major Apple Pear (Pyrus bretschneideri Rehd.) Orchards

Microbial communities are closely related to the overall health and quality of soil, but studies on microbial ecology in apple pear orchard soils are limited. In the current study, 28 soil samples were collected from three apple pear orchards, and the composition and structure of fungal and bacterial communities were investigated by high-throughput sequencing. The molecular ecological network showed that the keystone taxa of bacterial communities were Actinobacteria, Proteobacteria, Gemmatimonadetes, Acidobacteria, Nitrospirae, and Chloroflexi, and the keystone taxon of fungal communities was Ascomycota. Mantel tests showed that soil texture and pH were important factors shaping soil bacterial and fungal communities, and soil water soluble organic carbon (WSOC) and nitrate nitrogen (NO3--N) were also closely related to soil bacterial communities. Canonical correspondence analysis (CCA) and variation partition analysis (VPA) revealed that geographic distance, soil texture, pH, and other soil properties could explain 10.55%, 13.5%, and 19.03% of the overall variation in bacterial communities, and 11.61%, 13.03%, and 20.26% of the overall variation in fungal communities, respectively. The keystone taxa of bacterial and fungal communities in apple pear orchard soils and their strong correlation with soil properties could provide useful clues toward sustainable management of orchards.

Soil bacterial diversity and community structure of Suaeda glauca vegetation in the Hetao Irrigation District, Inner Mongolia, China

Exploring the bacterial community in the S. glauca rhizosphere was of great value for understanding how this species adapted to the saline-alkali environment and for the rational development and use of saline-alkali soils. In this study, high-throughput sequencing technology was used to investigate the diversity characteristics and distribution patterns of soil bacterial communities in the rhizosphere of S.glauca-dominated communities in the Hetao Irrigation Distract, Inner Mongolia, China. The relationships among bacterial characteristics, soil physicochemical properties and vegetation in four sampling sites were analyzed. The soil bacterial communities in the rhizosphere of S. glauca-dominated communities were mainly composed of 16 phyla (i.e., Proteobacteria, Actinobacteria, Bacteroidetes, Gemmatimonadetes, Chloroflexi, Acidobacteria, Firmicutes, Planctomycetes, Deinococcus-Thermus, Verrucomicrobia, Saccharibacteria, Cyanobacteria, Nitrospirae, JL-ETNP-Z39, Parcubacteria and Chlorobi), and these populations accounted for more than 99% of the total bacterial community. At the genus level, the main bacterial communities comprised Halomonas, Nitriliruptor, Euzebya and Pelagibius, which accounted for 15.70% of the total bacterial community. An alpha diversity analysis indicated that the richness and diversity of rhizosphere soil bacteria differed significantly among the sampling sites, and the bacterial richness and diversity indices of severe saline-alkali land were higher than those of light and moderate saline-alkali land. The principal component analysis (PCA) and linear discriminant analysis effect size (LEfSe) showed significant differences in the species composition of the rhizosphere soil bacterial community among different sampling sites. A correlation analysis showed that the number of bacterial species exhibited the highest correlation with the soil water content (SWC). The richness and evenness indices were significantly correlated with the SWC and SO4 2-, K+ and Mg2+ concentrations. The electrical conductivity (EC), soluble ions (Na+, CO3 2- + HCO3 -, K+, Ca2+, Mg2+, and SO4 2+), SWC and vegetation coverage (VC) were the main drivers affecting the changes in its community structure. The bacterial community in the rhizosphere of S. glauca enhanced the adaptability of S. glauca to saline-alkali environment by participating in the cycling process of nutrient elements, the decomposition of organic matter and the production of plant growth regulating substances. These results provided a theoretical reference for further study on the relationship among rhizosphere soil microorganisms and salt tolerance in halophytes.

Inhibition of Spartina alterniflora growth alters soil bacteria and their regulation of carbon metabolism

The state of growth of invasive species has a significant impact on the microbial regulation of the soil carbon (C) cycle. This study focused on the growth of Spartina alterniflora treated with imazapyr in the Tiaozini wetland of Jiangsu Province, China. The changes in soil bacterial structure, bacterial C metabolic activity, soil C, and regulation mechanism of soil C metabolic activity by biotic and abiotic factors were investigated. The results showed that soil bacterial diversity eventually decreased significantly (p < 0.05) along with significant changes in microbial structure (p < 0.05). Significant changes in soil physicochemical properties due to S. alterniflora growth inhibition were the key factors affecting the changes in the soil bacterial taxa composition (p < 0.05). Abiotic factors showed a greater effect on metabolic activities related to C fixation and biosynthesis of bacterial taxa than biotic factors (self-regulation). Additionally, bacterial taxa regulated soil C emission and degradation to a greater extent than abiotic factors. This study provides important information for understanding the regulators of C cycling in coastal wetland soil during the control of S. alterniflora invasion by imazapyr; moreover, it provides a scientific basis for the government to establish a prevention and control policy for S. alterniflora invasion. Understanding the complex interplay between abiotic and biotic factors is essential for developing effective strategies to manage soil C and mitigate the impacts of climate change.

Soil bacterial communities are influenced by soil chemical characteristics and dispersal limitation in commercial strawberry production systems

Bacterial communities play multiple functional roles in soil that have positive and negative feedbacks on plant health. However, relatively few studies have focused on the ecology of soil bacterial communities in commercial strawberry production systems. The objective of this study was to determine if ecological processes influencing soil bacterial communities are consistent among commercial strawberry production locations and plots within the same geographic region. Soil samples were collected using a spatially explicit design from three plots in two commercial strawberry production locations in the Salinas Valley region of California. Soil carbon, nitrogen, and pH were measured for each of the 72 soil samples and bacterial communities were characterized using 16 S rRNA sequencing. Multivariate analyses showed bacterial community composition was differentiated between the two strawberry production locations. Analyses of communities within plots demonstrated soil pH and nitrogen were significant predictors of bacterial community composition in one of the three sampled plots. Bacterial communities displayed spatial structure in two plots at one location based on a significant increase in community dissimilarity with increasing spatial distance. Null model analyses identified a lack of phylogenetic turnover among bacterial communities in all plots, but a greater frequency of dispersal limitation in the two plots where spatial structure was also observed. Overall, this work suggests that ecological factors influencing soil bacterial communities are not consistent among different strawberry production locations or plots which may impact the ability to predict or manage the effect of soil microbiomes on strawberry health.

Effect of different straw retention techniques on soil microbial community structure in wheat-maize rotation system

Rotational straw return technique is considered an effective measure for improving soil quality and maintaining soil microorganisms. However, there are few reports on the influence of wheat-maize crop rotation and straw-returning tillage on crop soil microbial communities in China. This study aimed to investigate how wheat or maize straw-incorporation practices affect bacterial and fungal communities under wheat-maize rotational farming practices. To clarify the effects of straw incorporation on microbial composition, microbial communities from soils subjected to different treatments were identified using high-throughput sequencing. Our results showed that, before corn planting, wheat and maize straw returning reduced bacterial density and increased their diversity but had no effect on fungal diversity. However, before wheat planting, returning wheat and corn stalks to the field increased the diversity of soil bacteria and fungi, whereas returning corn stalks to the field reduced the diversity of fungi and other microorganisms. Straw return significantly increased the relative abundance of Ascomycota in the first season and decreased it in the second season; however, in the second season, wheat straw return increased the relative abundance of Bradyrhizobium, which can promote the soil microbial nitrogen cycle and provide nitrogen to the soil. Wheat and maize straw return increased the relative abundance of Chaetomium, whereas, individually, they decreased the relative abundance. In addition, we detected two fungal pathogens (Fusarium and Trichoderma) under the two planting patterns and found that the relative abundance of pathogenic Fusarium increased with wheat straw return (FW and SW). Trichoderma increased after treatment with maize straw return before wheat planting (S group). These results suggest that wheat straw return (FW and SW) and maize straw return might have a negative impact on the pathogenic risk. Therefore, further studies are needed to determine how to manage straw returns in agricultural production.

Comparison and interpretation of freshwater bacterial structure and interactions with organic to nutrient imbalances in restored wetlands

Chemical oxygen demand to nitrogen (COD/N) and nitrogen to phosphorus (N/P) ratios have distinct effects on bacterial community structure and interactions. However, how organic to nutrient imbalances affect the structure of freshwater bacterial assemblages in restored wetlands remains poorly understood. Here, the composition and dominant taxa of bacterial assemblages in four wetlands [low COD/N and high N/P (LH), low COD/N and low N/P (LL), high COD/N and high N/P (HH), and high COD/N and low N/P (HL)] were investigated. A total of 7,709 operational taxonomic units were identified by high throughput sequencing, and Actinobacteria, Proteobacteria, and Cyanobacteria were the most abundant phyla in the restored wetlands. High COD/N significantly increased bacterial diversity and was negatively correlated with N/P (R 2 = 0.128; p = 0.039), and the observed richness (Sobs) indices ranged from 860.77 to 1314.66. The corresponding Chao1 and phylogenetic diversity (PD) values ranged from 1533.42 to 2524.56 and 127.95 to 184.63. Bacterial beta diversity was negatively related to COD/N (R 2 = 0.258; p < 0.001). The distribution of bacterial assemblages was mostly driven by variations in ammonia nitrogen (NH4 +-N, p < 0.01) and electrical conductivity (EC, p < 0.01), which collectively explained more than 80% of the variation in bacterial assemblages. However, the dominant taxa Proteobacteria, Firmicutes, Cyanobacteria, Bacteroidetes, Verrucomicrobia, Planctomycetes, Chloroflexi, and Deinococcus-Thermus were obviously affected by variation in COD/N and N/P (p < 0.05). The highest node and edge numbers and average degree were observed in the LH group. The co-occurrence networkindicated that LH promoted bacterial network compactness and bacterial interaction consolidation. The relationships between organic to nutrient imbalances and bacterial assemblages may provide a theoretical basis for the empirical management of wetland ecosystems.

Ratio of carbon and nitrogen in fertilizer treatment drives distinct rhizosphere microbial community composition and co-occurrence networks

Fertilization is the main strategy to accelerate vegetation restoration and improve the rhizosphere microbial community in the northeast China. However, the responses of rhizosphere microbial community structure, specific microbial community and symbiotic pattern to manure fertilization in grassland (alfalfa only) are not well clear. In this study, the variation of bacterial community structures in R_Manure (extracted liquid of fermented cow manure), E_Manure (extracted residue of fermented cow manure), F_Manure (full fermented cow manure), and Control (without fermented cow manure) collected from the rhizosphere microbial community of alfalfa were analyzed by the application of an Illumina HiSeq high-throughput sequencing technique. A total of 62,862 microbial operational taxonomic units (OTUs) were detected and derived from 21 phyla of known bacteria. The dominant bacteria in the rhizosphere include Proteobacteria (70.20%), Acidobacteria (1.24%), Actinobacteria (2.11%), Bacteroidetes (6.15%), Firmicutes (4.21%), and Chlorofexi (2.13%) accounting for 86% of the dominant phyla in all treatments. At the genus level, the dominant genus include NB1-j, Lysobacter, Alphaproteobacteria, Subgroup_6, Actinomarinales, Saccharimonadales, Aneurinibacillus, MO-CFX2, SBR1031, Caldilineaceae, and so on with the average relative abundance (RA) of 1.76%, 1.52%, 1.30%, 1.24%, 1.61%, 2.39%, 1.36%, 1.42%, 1.27%, and 1.03%, respectively. Bacterial diversities and community structures were significantly differentiated by different treatments of fertilization. The results of community structure composition showed that R_Manure treatment significantly increased the population abundance of Firmicutes, Chlorofexi, and Patescibacteria by 34.32%, 6.85%, and 2.70%, and decreased the population abundance of Proteobacteria and Actinobacteria by 16.83% and 1.04%, respectively. In addition, it showed that all treatments significantly resulted in an increase or decrease at the genus level. R_Manure had the higher richness and diversity of the bacterial community, with the greatest topology attributes of the co-occurrence networks. Through the analysis of the molecular ecological network (MENA), the co-occurrence networks had a shorter average path distance and diameter in R_Manure than in others, implying more stability to environmental changes. Redundancy analysis (RDA) showed that the ratio of carbon and nitrogen (C/N) was the main factor affecting rhizosphere microbial community composition while driving distinct rhizosphere bacterial community and its co-occurrence networks. The R_Manure associated with more C/N had relatively complex microbial co-occurrence network with a large number of nodes and edges, while the microbial network of others associated with less C/N had fewer taxa with loose mutual interactions. These results suggested that organic fertilizer with high C/N can regulate the rhizosphere microorganism, while high C/N can determine bacterial community structures, specific bacterial taxa, and their relationships with the nodule size of alfalfa. These significant changes can be used to evaluate soil fertility and fertilizer management in the artificial grassland system, while the potential biological indicators of the rhizosphere microbial community will play an important role in future eco-agriculture.

Succession of soil microbial community in a developing mid-channel bar: The role of environmental disturbance and plant community

Succession of microbial and plant communities is crucial for the development and the stability of soil ecological functions. The relative role of plant communities and environmental disturbance in shaping the microbial community in a newly established habitat remains unclear. In this study, a mid-channel bar (MCB) exposed to an environmental disturbance gradient in the Yangtze River was studied to explore the effects of such disturbance and plant community traits on the succession of the soil microbial community. Bulk and rhizospheric soils were collected from the MCB and classified according to their level of exposure to environmental disturbance: head, central and tail. These subsequently underwent high-throughput sequencing and interdomain ecological network (IDEN) analysis to identify and characterize the predominant microbial groups present in the soils at each disturbance level. Furthermore, at each site, the presence and distribution of the plant community was also noted. The present study demonstrated that both bulk soil nutrients and plant community exhibited significant spatial distribution dependent on the level of disturbance and this influenced the composition of the microbial community. In less eroded parts of the MCB, i.e., the central, nutrients accumulated, promoting growths of plants. This in turn encouraged a more diverse microbial community, dominated by the bacterial genus Pseudarthrobacter. Plant showed a stronger association with bulk soil microbial communities compared to rhizosphere soil microbial communities. Particularly, Triarrhena sacchariflora and Hemarthria altissima, present in sites of low disturbance, exhibiting a more extensive plant-microbe association. They thus played a key role in shaping the soil microbial community. In general, however, plant species did not directly determine the composition of the bacterial community, but instead altered the nutritive state of the soil to promote microbial growth. Such findings are of significant value for conservation practices of newly formed ecosystems, which requires an integrated understanding of the role of environmental disturbance and plants on soil microbial community assemblage.

Biofertilizers can enhance nitrogen use efficiency of sugarcane

Fertilizers are costly inputs into crop systems. To compensate for inefficiencies and losses from soil, farmers apply on average double the amount of nitrogen (N) fertilizer acquired by crops. We explored if N efficiency improves with biofertilizers formulated with organic waste, mineral N or plant growth-promoting rhizobacteria (PGPR). We compared treatments receiving mineral N fertilizer or biofertilizers at industry-recommended (100%) or lower (60%) N rates at two commercial sugarcane farms. Biofertilizer at the 60% N-rate generated promising results at one farm with significantly higher biomass and sugar yield than the no-N control, which matched the 100% mineral N treatment. This yield difference was accompanied by a shift in microbial diversity and composition. Correlation analysis confirmed that shifts in microbial communities were strongly linked to soil mineral N levels, as well as crop productivity and yield. Microbial co-occurrence networks further revealed that biofertilizer, including treatments with an added PGPR, can enhance bacterial associations, especially in the context of complex fungal networks. Collectively, the results confirm that biofertilizers have quantifiable effects on soil microbial communities in a crop system setting, which underscores the opportunities for biofertilizers to promote N use efficiency and the circular N economy.

Assembly and potential transmission of the lens culinaris seed microbiome

Soil is an important source of bacteria and fungi for the plant, but seeds can also provide microbial inocula through heritable or stochastic assembly. Seed-associated microbial communities can potentially interact with the host plant through multiple generations. Here, we assessed the impact of two different soil types on the seed microbiome assembly of seven lentil (Lens culinaris) genotypes under environmentally controlled conditions and examined the vertical transmission of bacterial communities from seed to seed across two generations. Bulk soil microbiomes and seed microbiomes were characterized using high-throughput amplicon sequencing of the bacterial 16S rRNA gene. Our results revealed that bacterial communities in the two soils differed significantly and that bacterial communities associated with seeds were significantly impacted by genotype (15%) in one of the soils. Co-occurrence of amplicon sequence variants (ASVs) between generations suggests members of the genera Cutibacterium, Methylobacterium, Sphingomonas, Streptococcus, and Tepidimonas are transmitted and preserved in lentil genotypes irrespective of the soil in which they were grown. Increasing our knowledge of how microbial communities carried by seeds are assembled, transmitted, and preserved offers a promising way for future breeding programs to consider microbial communities when selecting for more resilient and productive cultivars.

Phytoremediation of Cadmium Contaminated Soil Using Sesbania sesban L. in Association with Bacillus anthracis PM21: A Biochemical Analysis

Sustainable food production to feed nine to 10 billion people by 2050 is one of the greatest challenges we face in the 21st century. Due to anthropogenic activities, cadmium (Cd) contamination is ubiquitous with deleterious effects on plant and soil microbiota. In the current study, the phytoremediation potential of Sesbania sesban L. was investigated in Cd-spiked soil inoculated with Bacillus anthracis PM21. The Cd-spiked soil drastically reduced important plant attributes; however, inoculation of B. anthracis PM21 significantly (p ≤ 0.05) enhanced root length (17.21%), shoot length (15.35%), fresh weight (37.02%), dry weight (28.37%), chlorophyll a (52.79%), chlorophyll b (48.38%), and total chlorophyll contents (17.65%) at the Cd stress level of 200 mg/kg as compared to the respective control. In addition, bacterial inoculation improved superoxide dismutase (11.98%), peroxidase (12.16%), catalase (25.26%), and relative water content (16.66%) whereas it reduced proline content (16.37%), malondialdehyde content (12.67%), and electrolyte leakage (12.5%). Inoculated plants showed significantly (p ≤ 0.05) higher Cd concentration in the S. sesban root (118.6 mg/kg) and shoot (73.4 mg/kg) with a translocation (0.61) and bioconcentration factor (0.36), at 200 mg/kg Cd. Surface characterization of bacteria through Fourier transform infrared spectroscopy (FTIR) and scanning electron microscopy (SEM) predicted the involvement of various functional groups and cell surface morphology in the adsorption of Cd ions. Amplification of the CzcD gene in strain PM21, improved antioxidant activities, and the membrane stability of inoculated S. sesban plants conferred Cd tolerance of strain PM21. In addition, the evaluated bacterial strain B. anthracis PM21 revealed significant plant growth-promoting potential in S. sesban; thus, it can be an effective candidate for phyto-remediation of Cd-polluted soil.

Desert soil fungi isolated from Saudi Arabia: cultivable fungal community and biochemical production

Desert soils harbor fungi that have survived under highly stressed conditions of high temperature and little available moisture. This study was designed to survey the communities of cultivable fungi in the desert soils of the Arabian Peninsula and to screen the fungi for the potentially valuable antioxidants (flavonoids, phenols, saponins, steroids, tannins, terpenoids, and alkaloids) and enzymes (cellulase, laccase, lipase, protease, amylase, and chitinase). Desert soil was sampled at 30 localities representing different areas of Saudi Arabia and studied for physico-chemical soil properties. Five types of soil texture (sand, loamy sand, sandy loam, silty loam, and sandy clay loam) were observed. A total of 25 saprotrophic species was identified molecularly from 68 isolates. Our survey revealed 13 culturable fungal species that have not been reported previously from Arabian desert soils and six more species not reported from Saudi Arabian desert soils. The most commonly recorded genera were Aspergillus (isolated from 20 localities) and Penicillium (6 localities). The measurements of biochemicals revealed that antioxidants were produced by 49 and enzymes by 52 isolates; only six isolates did not produce any biochemicals. The highest biochemical activity was observed for the isolates Fusarium brachygibbosum and A. phoenicis. Other active isolates were A. proliferans and P. chrysogenum. The same species, for instance, A. niger had isolates of both high and low biochemical activities. Principal component analysis gave a tentative indication of a relationship between the biochemical activity of fungi isolated from soil and soil texture variables namely the content of silt, clay and sand. However, any generalizable relation between soil properties and fungal biochemical activities cannot be suggested. Each fungal isolate is probable to produce several antioxidants and enzymes, as shown by the correlation within the compound groups. Desert soil warrants further research as a promising source of biochemicals.

A walk on the dirt: soil microbial forensics from ecological theory to the crime lab

Forensics aims at using physical evidence to solve investigations with science-based principles, thus operating within a theoretical framework. This however is often rather weak, the exception being DNA-based human forensics that is well anchored in theory. Soil is a most commonly encountered, easily and unknowingly transferred evidence but it is seldom employed as soil analyses require extensive expertise. In contrast, comparative analyses of soil bacterial communities using nucleic acid technologies can efficiently and precisely locate the origin of forensic soil traces. However, this application is still in its infancy, and is very rarely used. We posit that understanding the theoretical bases and limitations of their uses is essential for soil microbial forensics to be judiciously implemented. Accordingly, we review the ecological theory and experimental evidence explaining differences between soil microbial communities, i.e. the generation of beta diversity, and propose to integrate a bottom-up approach of interactions at the microscale, reflecting historical contingencies with top-down mechanisms driven by the geographic template, providing a potential explanation as to why bacterial communities map according to soil types. Finally, we delimit the use of soil microbial forensics based on the present technologies and ecological knowledge, and propose possible venues to remove existing bottlenecks.

Influence of Peanut, Sorghum, and Soil Salinity on Microbial Community Composition in Interspecific Interaction Zone

Soil microorganisms play important roles in crop production and sustainable agricultural management. However, soil conditions and crop selection are key determining factors for soil microbial communities. This study investigated the effect of plant types and soil salinity on the microbial community of interspecific interaction zone (II) based on the sorghum/peanut intercropping system. Microbial community diversity and composition were determined through PacBio single molecule, real-time sequencing of 16S rDNA and internal transcribed spacer (ITS) genes. Results showed Proteobacteria, Bacteroidota, and Acidobacteriota to be the dominant bacterial phyla in IP, II, and IS, whereas Ascomycota, Basidiomycota, and Mucoromycota were the dominant fungal phyla. Under salt-treated soil conditions, the plants-specific response altered the composition of the microbial community (diversity and abundance). Additionally, the interspecific interactions were also helpful for maintaining the stability and ecological functions of microbial communities by restructuring the otherwise stable core microbiome. The phylogenetic structure of the bacterial community was greatly similar between IP and II while that of the fungal community was greatly similar between IP and IS; however, the phylogenetic distance between IP and IS increased remarkably upon salinity stress. Overall, salinity was a dominant factor shaping the microbial community structure, although plants could also shape the rhizosphere microenvironment by host specificity when subjected to environmental stresses. In particular, peanut still exerted a greater influence on the microbial community of the interaction zone than sorghum.

Persistence of Salmonella Typhimurium in apple-pear (Pyrus bretschneideri Rehd.) orchard soils influenced by bacterial communities and soil properties

2In this study, we investigated the persistence of Salmonella Typhimurium in 26 soil samples from apple-pear orchards in Yanji, Longjing and Helong in northeastern China. The time to reach detection limit (ttds) of Salmonella Typhimurium in soils varied from 20 to 120 days. Redundancy analysis and variation partition analysis elucidated that bacterial communities, clay content, pH, electrical conductivity (EC) salinity, and NO₃^--N could explain more than 85% of overall variation of the persistence behaviors. Results of structural equation models and Mantel tests revealed that clay content and EC displayed both direct and indirect effect on ttds, while NO₃^--N and pH exhibited direct and indirect effect on the survival patterns, respectively. Furthermore, Actinobacteria, Acidobacteria and Deltaproteobacteria at class level showed highly close correlations with ttds. Our results revealed that certain biotic and abiotic factors could greatly contribute to the overall persistence of Salmonella in apple-pear orchard soils.

Bacterial diversity patterns of desert dunes in the northeastern Qinghai-Tibet Plateau, China

Limited knowledge about the variation patterns of bacterial community composition in the sand and vegetative ecosystems confines our understanding regarding the contribution of the sand dune to desert areas. In this study, 454 pyrosequencing platforms were adopted to determine the community structure of bacteria and diversity of sand dunes in northeastern Qinghai-Tibet Plateau, China: 50 cm deep, rhizosphere, physical crusts, and biological crusts representing sand and vegetative ecosystems, respectively. The findings revealed significant variation in bacterial diversities and the structure of communities in the sand and vegetative ecosystems. The dominant bacterial phyla of sand and vegetative ecosystems were Firmicutes (47%), Actinobacteria (21%), Proteobacteria (16%), and Bacteroidetes (13%), while Lactococcus (50%) was found to be the dominant genus. Furthermore, samples with high alpha-diversity indices (Chao 1 and Shannon) for the vegetative ecosystem have the lowest modularity index and the largest number of biomarkers, with some exceptions. Redundancy analysis exhibited that environmental factors could explain 72% (phyla) and 67% (genera) of the bacterial communities, with EC, TC, and TOC being the major driving factors. This study expands our understanding of bacterial community composition in the desert ecosystem. The findings suggest that variations in the sand and vegetative ecosystems, such as those predicted by environmental factors, may reduce the abundance and diversity of bacteria, a response that likely affects the provision of key ecosystem processes by desert regions.

Soil bacterial diversity, structure, and function of Suaeda salsa in rhizosphere and non-rhizosphere soils in various habitats in the Yellow River Delta, China

Soil microorganisms play a key role in regulating the biogeochemical cycles of ecosystems. However, studies that quantitatively examine bacterial metabolic groups to predict the environmental and biological impacts are limited. In this research, we employed 16S rRNA gene sequencing on an Illumina MiSeq platform to analyze bacterial diversity, structure, function, and driving factors of Suaeda salsa in rhizosphere and non-rhizosphere soils in intertidal and supratidal habitats in the Yellow River Delta, China. Results showed that bacterial richness and Shannon diversity index of the rhizosphere soil were greater in the intertidal than in the supratidal habitat. Although the bacteria of the two habitats changed extremely in community structure, the bacterial groups related to carbohydrate metabolism (CM) and amino acid metabolism (AAM) had higher abundance than the other groups in both habitats. Furthermore, they were higher in the supratidal than the intertidal habitats, and bacterial groups associated with energy metabolism (EM) are opposite. Furthermore, bacterial diversity showed no significant difference between the rhizosphere and non-rhizosphere soils. In the intertidal habitat, the rhizosphere soil had higher EM but lower AAM and CM than the non-rhizosphere soil, which indicated that bacterial structure and function were obviously influenced by the root exudates of S. salsa under flooding and salt stresses. Redundancy analysis showed that the dominant phyla were significantly affected by available phosphorus (51.0%), total potassium (32.2%), moisture content (28.1%), available potassium (25.3%), electrical conductivity (24.2%), total nitrogen (22.8%), total carbon (21.9%), and soil organic matter (21.0%). Overall, the findings provide important insights into the roles of bacterial groups in coastal wetland under climate changes.

Different types of agricultural land use drive distinct soil bacterial communities

Biogeographic patterns in soil bacterial communities and their responses to environmental variables are well established, yet little is known about how different types of agricultural land use affect bacterial communities at large spatial scales. We report the variation in bacterial community structures in greenhouse, orchard, paddy, and upland soils collected from 853 sites across the Republic of Korea using 16S rRNA gene pyrosequencing analysis. Bacterial diversities and community structures were significantly differentiated by agricultural land-use types. Paddy soils, which are intentionally flooded for several months during rice cultivation, had the highest bacterial richness and diversity, with low community variation. Soil chemical properties were dependent on agricultural management practices and correlated with variation in bacterial communities in different types of agricultural land use, while the effects of spatial components were little. Firmicutes, Chloroflexi, and Acidobacteria were enriched in greenhouse, paddy, and orchard soils, respectively. Members of these bacterial phyla are indicator taxa that are relatively abundant in specific agricultural land-use types. A relatively large number of taxa were associated with the microbial network of paddy soils with multiple modules, while the microbial network of orchard and upland soils had fewer taxa with close mutual interactions. These results suggest that anthropogenic agricultural management can create soil disturbances that determine bacterial community structures, specific bacterial taxa, and their relationships with soil chemical parameters. These quantitative changes can be used as potential biological indicators for monitoring the impact of agricultural management on the soil environment.

Microbial Diversity of Some Sabkha and Desert Sites in Saudi Arabia

Several studies isolated fungal and bacterial species from extreme environments, such as Sabkha and hot deserts, as their natural habitat, some of which are of medicinal importance. Current research aimed investigating the microbial (fungi and bacteria) diversity and abundance in Sabkha and desert areas in Saudi Arabia. Soil samples from nine different geographical areas (Al-Aushazia lake, AlQasab, AlKasar, Tabuk, Al-Kharj, Al-Madina, Jubail, Taif and Abqaiq) were collected and cultured for microbial isolation. Isolated fungi and bacteria were identified by molecular techniques (PCR and sequencing). Based on 18S rDNA sequencing, 203 fungal species belonging to 33 genera were identified. The most common fungal genera were Fusarium, Alternaria, Chaetomium, Aspergillus Cochliobolus and Pencillium, while the most common species were Chaetomium globosum and Fusarium oxysporum. By 16S rDNA sequencing 22 bacterial species belonging to only two genera, Bacillus and Lactobacillus, were identified. The most commonly isolated bacterial species were Bacillus subtilis and Lactobacillus murinus. Some fungal species were confined to specific locations, such as Actinomyces elegans, Fusarium proliferatum, Gymnoascus reesii and Myzostoma spp. that were only isolated from Al-Aushazia soil. AlQasab soil had the highest microbial diversity among other areas with abundances of 23.5% and 4.4% of total fungi, and bacteria, respectively. Findings of this study show a higher degree of fungal diversity than that of bacteria in all studied areas. Further studies needed to investigate the connection between some isolated species and their habitat ecology, as well as to identify those of medicinal importance.

Soil fungal taxonomic diversity along an elevation gradient on the semi-arid Xinglong Mountain, Northwest China

Elevation gradients, often regarded as "natural experiments or laboratories", can be used to study changes in the distribution of microbial diversity related to changes in environmental conditions that typically occur over small geographical scales. We exploited this feature by characterizing fungal composition and diversity along an elevation gradient on Xinglong Mountain, northwest China. For this, we used MiSeq sequencing to obtain fungal sequences and clustered them into operational taxonomic units (OTUs). In total, we obtained 1,203,302 reads, 133,700 on average in each sample of soil collected at three selected elevations (2807, 3046, and 3536 m). The reads were assigned to 2192 OTUs. Inconsistent variations were observed in fungal alpha-diversity in samples from the three elevations. However, Principal Coordinate Analysis based on Bray-Curtis and UniFrac (weighted and unweighted) distance metrics revealed that fungal communities in soil samples from 3046 and 3536 m elevations were most similar. Principal Component Analysis based on relative abundances of shared OTUs confirmed that OTUs in samples from 3536 m elevation were more closely related to OTUs from 3046 m than samples from 2807 m elevation. Ascomycota, Basidiomycota, Glomeromycota, Cercozoa and Chytridiomycota were the most abundant fungal phyla across the elevation gradient. Our study also provides valuable indications of relations between fungal communities and an array of soil chemical properties, and variations in fungal taxonomic diversity across a substantial elevation gradient.

Interaction between Fungal Communities, Soil Properties, and the Survival of Invading E. coli O157:H7 in Soils

Pathogens that invade into the soil cancontaminate food and water, andinfect animals and human beings. It is well documented that individual bacterial phyla are well correlated with the survival of E. coliO157 (EcO157), while the interaction betweenthe fungal communities and EcO157 survival remains largely unknown. In this study, soil samples from Tongliao, Siping, and Yanji in northeast China were collected and characterized. Total DNA was extracted for fungal and bacterial community characterization. EcO157 cells were spiked into the soils, and their survival behavior was investigated. Results showed that both fungal and bacterial communities were significantly correlated (p < 0.01) with the survival of EcO157 in soils, and the relative abundances of fungal groups (Dothideomycetes and Sordariomycetes) and some bacterial phyla (Acidobacteria, Firmicutes, gamma- and delta-Proteobacteria)weresignificantly correlated with ttds (p < 0.01). Soil pH, EC (electric conductance) salinity, and water-soluble nitrate nitrogen were significantly correlated with survival time (time to reach the detection limit, ttd) (p < 0.05). The structural equation model indicated that fungal communities could directly influence ttds, and soil properties could indirectly influence the ttds through fungal communities. The first log reduction time (δ) was mainly correlated with soil properties, while the shape parameter (p) was largely correlated with fungal communities. Our data indicated that both fungal and bacterial communities were closely correlated (p < 0.05)with the survival of EcO157 in soils, and different fungal and bacterial groups might play different roles. Fungal communities and bacterial communities explained 5.87% and 17.32% of the overall variation of survival parameters, respectively. Soil properties explained about one-third of the overall variation of survival parameters. These findings expand our current understanding of the environmental behavior of human pathogens in soils.

High abundance of Ralstonia solanacearum changed tomato rhizosphere microbiome and metabolome

BACKGROUND

Rhizosphere microbiome is dynamic and influenced by environment factors surrounded including pathogen invasion. We studied the effects of Ralstonia solanacearum pathogen abundance on rhizosphere microbiome and metabolome by using high throughput sequencing and GC-MS technology.

RESULTS

There is significant difference between two rhizosphere bacterial communities of higher or lower pathogen abundance, and this difference of microbiomes was significant even ignoring the existence of pathogen. Higher pathogen abundance decreased the alpha diversity of rhizosphere bacterial community as well as connections in co-occurrence networks. Several bacterial groups such as Bacillus and Chitinophaga were negatively related to the pathogen abundance. The GC-MS analysis revealed significantly different metabolomes in two groups of rhizosphere soils, i.e., the rhizosphere soil of lower harbored more sugars such as fructose, sucrose and melibiose than that in high pathogen abundance.

CONCLUSIONS

The dissimilar metabolomes in two rhizosphere soils likely explained the difference of bacterial communities with Mantel test. Bacillus and Chitinophaga as well as sugar compounds negatively correlated with high abundance of pathogen indicated their potential biocontrol ability.

Soil multifunctionality is affected by the soil environment and by microbial community composition and diversity

Microorganisms are critical in mediating carbon (C) and nitrogen (N) cycling processes in soils. Yet, it has long been debated whether the processes underlying biogeochemical cycles are affected by the composition and diversity of the soil microbial community or not. The composition and diversity of soil microbial communities can be influenced by various environmental factors, which in turn are known to impact biogeochemical processes. The objectives of this study were to test effects of multiple edaphic drivers individually and represented as the multivariate soil environment interacting with microbial community composition and diversity, and concomitantly on multiple soil functions (i.e. soil enzyme activities, soil C and N processes). We employed high-throughput sequencing (Illumina MiSeq) to analyze bacterial/archaeal and fungal community composition by targeting the 16S rRNA gene and the ITS1 region of soils collected from three land uses (cropland, grassland and forest) deriving from two bedrock forms (silicate and limestone). Based on this data set we explored single and combined effects of edaphic variables on soil microbial community structure and diversity, as well as on soil enzyme activities and several soil C and N processes. We found that both bacterial/archaeal and fungal communities were shaped by the same edaphic factors, with most single edaphic variables and the combined soil environment representation exerting stronger effects on bacterial/archaeal communities than on fungal communities, as demonstrated by (partial) Mantel tests. We also found similar edaphic controls on the bacterial/archaeal/fungal richness and diversity. Soil C processes were only directly affected by the soil environment but not affected by microbial community composition. In contrast, soil N processes were significantly related to bacterial/archaeal community composition and bacterial/archaeal/fungal richness/diversity but not directly affected by the soil environment. This indicates direct control of the soil environment on soil C processes and indirect control of the soil environment on soil N processes by structuring the microbial communities. The study further highlights the importance of edaphic drivers and microbial communities (i.e. composition and diversity) on important soil C and N processes.

The drivers of bacterial community underlying biogeographical pattern in Mollisol area of China

In order to better understand the composition and driving factors of the bacterial community in Mollisols, we selected 9 representative facility agricultural lands in Mollisol area of China for sampling, and described it on a larger spatial scale. Soil bacterial community structure in these 9 regions (determined by high-throughput sequencing analysis) showed significant differences at the genus level. The correlation between bacterial community composition and soil properties, contaminants and geographical latitude showed that the diversity of bacterial community was still strongly correlated with pH and SOM under the influence of phthalates (P < 0.05). Principal component Analysis (PCA) showed that soil properties (i.e. pH, organic matter, stacking density, the content of nitrogen, potassium, phosphorus) and PAEs level rather than geographic latitude were main drivers of differences in bacterial community structure. These factors account for 73.04% of the total variation of the bacterial community. Among them, PAEs act as a typical pollutant is the main factor driving the composition of bacterial community in facility agriculture Mollisols. This shows that PAEs is a potential pollution risk factor, which has important guiding significance for the sustainable and healthy development of agriculture in Mollisol area.

Effects of Agricultural Management on Rhizosphere Microbial Structure and Function in Processing Tomato Plants

Agricultural management practices affect bulk soil microbial communities and the functions they carry out, but it remains unclear how these effects extend to the rhizosphere in different agroecosystem contexts. Given close linkages between rhizosphere processes and plant nutrition and productivity, understanding how management practices impact this critical zone is of great importance to optimize plant-soil interactions for agricultural sustainability. A comparison of six paired conventional-organic processing tomato farms was conducted to investigate relationships between management, soil physicochemical parameters, and rhizosphere microbial community composition and functions. Organically managed fields were higher in soil total N and NO₃-N, total and labile C, plant Ca, S, and Cu, and other essential nutrients, while soil pH was higher in conventionally managed fields. Differential abundance, indicator species, and random forest analyses of rhizosphere communities revealed compositional differences between organic and conventional systems and identified management-specific microbial taxa. Phylogeny-based trait prediction showed that these differences translated into more abundant pathogenesis-related gene functions in conventional systems. Structural equation modeling revealed a greater effect of soil biological communities than physicochemical parameters on plant outcomes. These results highlight the importance of rhizosphere-specific studies, as plant selection likely interacts with management in regulating microbial communities and functions that impact agricultural productivity.IMPORTANCE Agriculture relies, in part, on close linkages between plants and the microorganisms that live in association with plant roots. These rhizosphere bacteria and fungi are distinct from microbial communities found in the rest of the soil and are even more important to plant nutrient uptake and health. Evidence from field studies shows that agricultural management practices such as fertilization and tillage shape microbial communities in bulk soil, but little is known about how these practices affect the rhizosphere. We investigated how agricultural management affects plant-soil-microbe interactions by comparing soil physical and chemical properties, plant nutrients, and rhizosphere microbial communities from paired fields under organic and conventional management. Our results show that human management effects extend even to microorganisms living in close association with plant roots and highlight the importance of these bacteria and fungi to crop nutrition and productivity.

Variations in Soil Functional Fungal Community Structure Associated With Pure and Mixed Plantations in Typical Temperate Forests of China

Forest plants are in constant contact with the soil fungal community, which plays an important role in the circulation of nutrients through forest ecosystems. The objective of this study was to evaluate the fungal diversity in soil and elucidate the ecological role of functional fungal communities in forest ecosystems using soil samples from seven different plantations in northeastern China. Our results showed that the fungal communities were dominated by the phyla Ascomycota, Basidiomycota, and Mortierellomycota, and the mixed plantation of Fraxinus mandshurica and Pinus koraiensis had a soil fungal population clearly divergent from those in the other plantations. Additionally, the mixed plantation of F. mandshurica and P. koraiensis, which was low in soil nutrients, contained a highly diverse and abundant population of ectomycorrhizal fungi, whereas saprophytic fungi were more abundant in plantations with high soil nutrients. Redundancy analysis demonstrated a strong correlation between saprophytic fungi and the level of soil nutrients, whereas ectomycorrhizal fungi were mainly distributed in soils with low nutrient. Our findings provide insights into the importance of functional fungi and the mediation of soil nutrients in mixed plantations and reveal the effect of biodiversity on temperate forests.

The Variation of the Soil Bacterial and Fungal Community Is Linked to Land Use Types in Northeast China

From the west to the east across Northeast China, there are three major land use types, ranging from agricultural-pastoral interlaced land, crop land, and forest land. The soil microbial community of each land use type has been reported; however, a thorough comparison of the soil microbial ecology of soils from each land use type has not been made. In the current study, soil samples from agricultural-pastoral land, crop land, and an artificial economic forest were collected from Tongliao, Siping, and Yanji, respectively. The structure and composition of bacterial and fungal communities was investigated by a next generation sequencing protocol, and soil physicochemical properties were also determined. Pair-wise analysis showed some soil parameters were significantly different between agricultural-pastoral land and crop land or forest land, while those soil parameters shared more similarities in crop land and forest land soils. Principal coordinates analysis and dissimilarity analyses jointly indicated that bacterial and fungal communities from each sampling site were quite different. Canonical correspondence analysis and a partial Mantel test showed that the community structures of bacteria and fungi were mainly affected by clay, pH, water soluble organic carbon (WSOC), and total soluble nitrogen (TN). Co-occurrence network analysis and the associated topological features revealed that the network of the bacterial community was more complex than that of the fungal community. Clay, pH, WSOC, and NH4+-N were major drivers and pH and WSOC were major factors in shaping the network of the bacterial community and the fungal community, respectively. In brief, our results indicated that microbial diversity, co-occurrence network patterns, and their shaping factors differed greatly among soils of distinct land use types in Northeast China. Our data also provided insights into the sustainable use of soils under different land use types.

Applying microbial biogeography in soil forensics

The ubiquity, heterogeneity and transferability of soil makes it useful as evidence in criminal investigations, especially using new methods that survey the microbial DNA it contains. However, to be used effectively and reliably, more needs to be learned about the natural distribution patterns of microbial communities in soil. In this study we examine these patterns in detail, at local to regional scales (2 m-260 km), across an environmental gradient in three different soil types. Geographic location was found to be more important than soil type in determining the microbial community composition: communities from the same site but different soil types, although significantly different from each other, were still much more similar to each other than were communities from the same soil type but from different sites. At a local scale (25-1000 m), distance-decay relationships were observed in all soil types: the farther apart two soil communities were located, even in the same soil type, the more they differed. At regional-scale distances (1-260 km), differences between communities did not increase with increased geographic distance between them, and the dominant factor determining the community profile was the physico-chemical environment, most notably annual precipitation (R² = 0.69), soil sodium (R² = 0.49) and soil ammonium (R² = 0.47) levels. We introduce a likelihood-ratio framework for quantitative evaluation of soil microbial DNA profile evidence in casework. In conclusion, these profiles, along with detailed knowledge of natural soil microbial biogeography, provide valuable forensic information on soil sample comparison and allow the determination of approximate source location on large (hundreds of km) spatial scales. Moreover, at small spatial scales it may enable pinpointing the source location of a sample to within at least 25 m, regardless of soil type and environmental conditions.

Soil productivity and structure of bacterial and fungal communities in unfertilized arable soil

Soil productivity is strongly influenced by the activities of microbial communities. However, it is not well understood how community structure, including its richness, mass, and composition, influences soil functions. We investigated the relationships between soil productivity and microbial communities in unfertilized arable soils extending over 1000 km in eastern Japan. Soil properties, including C turnover rate, N mineralization rate, microbial C, and various soil chemical properties, were measured. Soil bacterial and fungal communities were analyzed by Illumina's MiSeq using 16S rRNA and ITS regions. In addition, root microbial communities from maize grown in each soil were also investigated. Soil bacterial communities shared many operational taxonomic units (OTUs) among farms. An ordination plot based on correspondence analysis revealed convergent distribution of soil bacterial communities across the farms, which seemed to be a result of similar agricultural management practices. Although fungal communities showed lower richness and a lower proportion of shared OTUs than bacterial communities, community structure between the farms tended to be convergent. On the other hand, root communities had lower richness and a higher abundance of specific taxa than the soil communities. Two soil functions, decomposition activity and soil productivity, were extracted by principal component analysis (PCA) based on eight soil properties. Soil productivity correlated with N mineralization rate, P2O5, and maize growth, but not with decomposition activity, which is characterized by C turnover rate, soil organic C, and microbial mass. Soil productivity showed a significant association with community composition, but not with richness and mass of soil microbial communities. Soil productivity also correlated with the abundance of several specific taxa, both in bacteria and fungi. Root communities did not show any clear correlations with soil productivity. These results demonstrate that community composition and abundance of soil microbial communities play important roles in determining soil productivity.

Do composition and diversity of bacterial communities and abiotic conditions of spring water reflect characteristics of groundwater ecosystems exposed to different agricultural activities?

Modern agricultural practices have undeniably increased global food production. On the other hand, agricultural practices not only lead to a degradation of natural ecosystems but also affect the functioning of ecosystems and the related services they provide. Even though impacts of anthropogenic activities vary across ecosystems, freshwater ecosystems are among those affected to a higher degree. In comparison to surface water ecosystems, groundwater ecosystems are less affected by anthropogenic pollutants, as the overlaying soil retains organic and inorganic substances. However, it has become evident that the excessive use of fertilizers has led to the eutrophication of many aquifers. Bacterial communities, which significantly contribute to the cycling of matter due to their metabolic capacities, are prone to environmental perturbations, and structural variation of bacterial communities may consequently affect the functioning of groundwater ecosystems. Our present paper intends to evaluate the impact of anthropogenic activities on environmental conditions as well as on the structural properties of bacterial communities in groundwater. We repeatedly sampled emerging groundwater at five spring sites belonging to different catchments and determined the concentration of abiotic variables as well as the diversity and composition of bacterial communities on a local scale. We hypothesized that anthropogenic activities influence the concentration of abiotic variables, especially of nitrate, as well as the composition and diversity of bacterial communities in groundwater. Our results show that underground spring catchment areas only slightly differ regarding the concentration of abiotic variables as well as the structure of bacterial communities. Furthermore, abiotic variables, presumably influenced by anthropogenic activities, do not correlate with the diversity and composition of bacterial communities. Although supported only by circumstantial evidence, we suggest that upwelling groundwater from the deeper aquifer affects the diversity and composition of bacterial communities, and we argue that bacterial communities act as useful indicators for environmental changes.

Vertical variation of a black soil's properties in response to freeze-thaw cycles and its links to shift of microbial community structure

Soil freeze-thaw cycles (FTCs) change soil physical, chemical, and biological properties, however information regarding their vertical variations in response to FTCs is limited. In this work, black soil (silty loam) packed soil columns were exposed to 8 FTCs, and soil properties were determined for each of vertical layer of soil columns. The results revealed that after FTCs treatment, moisture and electrical conductivity (EC) salinity tended to increase in upper soil layers. Increments of ammonium nitrogen (NH₄⁺-N) and nitrate nitrogen (NO₃^--N) in top layers (0-10cm) were greater than those in other layers, and increments of water soluble organic carbon (WSOC) and decrease of microbial biomass carbon (MBC) in middle layers (10-20cm) were greater than those in both ends. Overall, microbial community structure was mainly influenced by soil physical properties (moisture and EC) and chemical properties (pH and WSOC). For bacterial (archaeal) and fungal communities, soil physical properties, chemical properties and their interaction explained 79.73% and 82.66% of total variation, respectively. Our results provided insights into the vertical variation of soil properties caused by FTCs, and such variation had a major impact on the change of structure and composition of soil bacterial and fungal communities.

Wood Ash Induced pH Changes Strongly Affect Soil Bacterial Numbers and Community Composition

Recirculation of wood ash from energy production to forest soil improves the sustainability of this energy production form as recycled wood ash contains nutrients that otherwise would be lost at harvest. In addition, wood-ash is beneficial to many soils due to its inherent acid-neutralizing capabilities. However, wood ash has several ecosystem-perturbing effects like increased soil pH and pore water electrical conductivity both known to strongly impact soil bacterial numbers and community composition. Studies investigating soil bacterial community responses to wood ash application remain sparse and the available results are ambiguous and remain at a general taxonomic level. Here we investigate the response of bacterial communities in a spruce forest soil to wood ash addition corresponding to 0, 5, 22, and 167 t wood ash ha^-1. We used culture-based enumerations of general bacteria, Pseudomonas and sporeforming bacteria combined with 16S rRNA gene amplicon sequencing to valuate soil bacterial responses to wood ash application. Results showed that wood ash addition strongly increased soil pH and electrical conductivity. Soil pH increased from acidic through neutral at 22 t ha^-1 to alkaline at 167 t ha^-1. Bacterial numbers significantly increased up to a wood ash dose of 22 t ha^-1 followed by significant decrease at 167 t ha^-1 wood ash. The soil bacterial community composition changed after wood ash application with copiotrophic bacteria responding positively up to a wood ash dose of 22 t ha^-1 while the adverse effect was seen for oligotrophic bacteria. Marked changes in bacterial community composition occurred at a wood ash dose of 167 t ha^-1 with a single alkaliphilic genus dominating. Additionally, spore-formers became abundant at an ash dose of 167 t ha^-1 whereas this was not the case at lower ash doses. Lastly, bacterial richness and diversity strongly decreased with increasing amount of wood ash applied. All of the observed bacterial responses can be directly explained by the wood ash induced changes in pH, electrical conductivity and the addition of wood ash inherent nutrients.