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Changes in soil physicochemical properties and bacterial community composition were investigated six years after biochar amendment at 0%, 4%, 8% and 12% (w/w), which were coded as C0, C1, C2 and C3, respectively. Results showed that some soil characteristics were sustainable, as they were still affected by biochar addition after six years. Compared to the control, biochar-treated soils had higher pH, total carbon (TC), C/N, total nitrogen (TN), available phosphorus (AP) and available potassium (AK). Soil pH, C/N and the content of TC, TN and AK all increased along with the increase of biochar dosage. The results of Illumina MiSeq sequencing demonstrated that biochar enhanced soil bacteria diversity and modified the community composition over time. The relative abundance of Nitrospirae and Verrucomicrobia phylum increased but that of Acidobacteria phylum decreased significantly in biochar amended soils. The addition of biochar also enriched some bacterial genera, such as uncultured Nitrosomonadace, uncultured Gemmatimonadac, uncultured Nitrospiraceae and Magnetovibrio. In particular, the relative abundance of uncultured Nitrospiraceae was enhanced by 16.9%, 42.8% and 73.6% in C1, C2 and C3, respectively, compared to C0. Biochar has a potential role in enhancing the abundance of bacteria involved in N cycling. Soil pH, TC, TN, TK and AK, were closely related to alterations in the composition of the soil bacterial community. Meanwhile, these soil properties were significantly influenced by biochar amendment, which indicates that biochar affected the soil microbial community indirectly by altering the soil characteristics in the long term.

This research aimed to study changes in the diversity of the soil bacterial community in a jujube forest with different years of abandonment. To this end, we took the mountain jujube forest with different abandoned years (1 a, 3 a, 6a and 20 a) in the Qijiashan jujube experimental demonstration base in Yanchuan County as the research object; we used Illumina Miseq high-throughput sequencing technology to analyze the changes in the soil bacterial community structure and reveal the key environmental drivers of bacterial community variation in the abandoned jujube forest in the study area. The results showed the following findings: (1) Phylum Actinomycetota (34%), Proteobacteria (29%), and Acidobacteriota (13%) were the dominant phyla of the soil bacterial community in the abandoned jujube forest. (2) Abandonment altered the composition of soil bacteria at the OTU level in jujube plantations. (3) There are differences in the soil bacterial community structure across different periods of abandonment in the jujube forest. (4) Soil water content is the main factor affecting the bacterial community structure of the abandoned jujube forest. There are differences in the soil water content of abandoned woodlands, which affects the community structure of soil microorganisms.

Our study, which was conducted in the desert grassland of Ningxia in China (E 107.285, N 37.763), involved an experiment with five levels of annual precipitation 33% (R33), 66% (R66), 100% (CK), 133% (R133), 166% (R166) and two temperature levels (inside Open-Top Chamber (OTC) and outside OTC). Our objective was to determine how plant, soil bacteria, and fungi diversity respond to climate change. Our study suggested that plant α-diversity in CK and TCK were significantly higher than that of other treatments. Increased precipitation promoted root biomass (RB) growth more than aboveground living biomass (ALB). R166 promoted the biomass of Agropyron mongolicum the most. In the fungi communities, temperature and precipitation interaction promoted α-diversity. In the fungi communities, the combination of increased temperature and natural precipitation (TCK) promoted β-diversity the most, whose distance was determined to be 25,124 according to PCA. In the bacteria communities, β-diversity in CK was significantly higher than in other treatments, and the distance was determined to be 3010 according to PCA. Soil bacteria and fungi α- and β-diversity, and ALB promoted plant diversity the most. The interactive effects of temperature and precipitation on C, N, and P contents of plants were larger than their independent effects.

Microbes may play an important role in the sugarcane leaf degradation and nutrient conversion process. Soil bacterial communities are more or less involved in material transformation and nutrient turnover. In order to make better use of the vast sugarcane leaf straw resources and reduce the overuse of chemical fertilizers in the subtropical red soil region of Guangxi, a pot experiment, with three sugarcane leaf return (SLR) amounts [full SLR (FS), 120 g/pot; half SLR (HS), 60 g/pot; and no SLR (NS)] and three fertilizer reduction (FR) levels [full fertilizer (FF), 4.50 g N/pot, 3.00 g P2O5/pot, and 4.50 g K2O/pot; half fertilizer (HF), 2.25 g N/pot, 1.50 g P2O5/pot, and 2.25 g K2O/pot; and no fertilizer (NF)], was conducted to assess the interactions of different SLR amounts and chemical FR levels in the soil bacterial network and the relationship between the soil properties and bacterial network by using Illumina Miseq high-throughput sequencing technology. According to the results of the soil bacterial community compositions and diversity, the soil bacterial network was changed during maize growth. SLR exerted a stronger effect on soil bacterial function than FR. Returning the sugarcane leaf to the field increased the diversity of the soil bacteria network. The bacterial communities were consistently dominated by Acidobacteria, Actinobacteria, and Bacteroidetes across all treatments, among which Actinobacteria was the most abundant bacteria type by almost 50% at the phylum level. The analysis results of the experimental factor on maize growth showed that the effect of SLR was lower than that of FR; however, this was opposite in the soil bacterial community structure and diversity. The soil bacterial network was significantly correlated with the soil total K, available N and organic matter contents, and EC. The soil bacteria community showed different responses to SLR and FR, and the FF in combination with FS partly increased the complexity of the soil bacteria network, which can further benefit crop production and soil health in the red soil region.

The Special Issue “Genetic Diversity of Soil Bacterial Communities” collected research and review articles addressing some relevant and unclear aspects of the composition and functioning of bacterial communities in rich or marginal agricultural soils, in field trials as well as in laboratory-scale experiments, at different latitudes and under different types of management.

To explore the diversity of soil bacteria and changes in the bacterial community structure of Chinese fir plantations of different generations and developmental stages, the genetic diversity of soil bacteria was studied using the 454 sequencing technology. The results showed that the bacterial genetic diversity and community structure of Chinese fir plantation plots under monoculture planting and rotation planting practices were as follows: the Shannon diversity indices of first-generation young plantation of Chinese fir plantations (FYC), second-generation young plantation (SYC), and third-generation young plantation (TYC) initially decreased and then increased to 8.45, 8.1, and 8.43, respectively. Due to different management and tending measures, the phyla showing considerable differences in relative abundance were Cyanobacteria, Nitrospirae, Fibrobacteres, Thermotogae, and Planctomycetes. The bacterial genetic diversity and community structure of Chinese fir plantations at different developmental stages were as follows: the bacterial diversity and the number of operational taxonomic units (OTUs) decreased with increasing forest age; with the increasing forest age of Chinese fir, the bacteria with considerable differences in the relative abundance were Burkholderiales, Xanthomonadales, Ktedonobacteria, Nitrosomonadales, Anaerolineae, and Holophagae. The predominant bacteria of the Chinese fir plantations were Acidothermus, Bradyrhizobium, Lactococcus, Planctomyces, Sorangium, and Bryobacter.

Acid mine drainage (AMD) barrens result from the death of vegetation resulting from overland flow of acidic metal-rich waters emerging from abandoned underground mines. In 2006, a restoration experiment was conducted by our research group at a 50-year-old AMD barrens to determine whether vegetation could be established by altering, rather than removing, surface layers of acidic iron-rich precipitates at the site which is representative of other mining-degraded areas. This dissertation builds on the investigation initiated in 2006 in the zone where subsurface AMD flow was most shallow and focuses on non-reclaimed (control) precipitates covered by mossy biological crusts and reclaimed precipitates sustaining vegetation. Iron (Fe) biogeochemistry in AMD precipitates was studied to gain an understanding of potential losses of redox-active metals after plant-based reclamation. As mobility of redox-active metals can be increased by enhanced microbial activity in the rooting zones of growing plants, we compared the forms of Fe in the reclaimed and control precipitates five years post-reclamation. Since Fe is the most abundant metal in many mine drainages, root exudation by growing plants could stimulate Fe(III)-reducing activity in rhizospheres, resulting in losses of soluble Fe(II) from the system. Precipitates were sampled from moist yet unsaturated surface sections (8-cm depth) excised from replicate plots. Ferrozine tests of extracts indicated that Fe(II) concentrations were three- to five-fold higher in reclaimed precipitates than in control precipitates. Microbial communities inhabiting AMD-impacted environments have been more extensively studied in aqueous rather than terrestrial systems. Our reclamation study provided the opportunity to gain insights into AMD-derived bacterial and eukaryotic communities in unsaturated, edaphic habitats. Precipitates of the same types as described for the Fe-biochemistry study (RR, RB, CC, and CB) were collected six years post-reclamation. At the time of sampling, all four precipitate types had similar pH levels (2.5-2.7) because reclaimed precipitates had gradually become more acidic following the one-time lime application in 2006. Bacterial and eukaryotic diversity were assessed using 454 pyrosequencing of 16S rRNA (V1-V3/V5 region) and the 18S rRNA (V4-V5 region) genes. Contrary to our projections we observed high bacterial and eukaryotic diversity across all samples. For bacterial libraries, we recovered a total of 3,150 operational taxonomic units (OTUs) at 97% similarity. Approximately 50% of these were exclusively found in reclaimed precipitates (RR, RB or both), 33% were unique to control precipitates (CC, CB, or both), and 6% were shared among the four precipitate types. Nineteen phyla were identified in the four type of precipitates and 13 of these were found in all samples. Proteobacteria comprised the most abundant representatives in reclaimed precipitates while Acidobacteria were more abundant in root-and crust-adherent precipitates. Eukaryotic diversity was also higher in reclaimed precipitates than in control precipitates, reflecting the positive influence of plant establishment. Of the total 494 OTUs identified at the 95% similarity level, about 62% were found exclusively in reclaimed precipitates (RR, RB or both), 20% were unique to control precipitates (CC, CB, or both), and only 7% were shared among the four precipitate types. Since libraries from control precipitates were dominated by bryophyte sequences, these and other macroeukaryotic sequences were removed before calculating the percentages of microeukaryotic taxa in each precipitate. The main microeukaryotic taxa identified in reclaimed precipitates were Basidiomycota, 48% in RR and 39% in RB. In contrast, Ascomycota were more abundant in control precipitates, 50% in CC and 18% in CB, reflecting a shift in fungal community composition following reclamation. Many taxa reported to be abundant in water-impacted AMD habitats were either very low in abundance or not detected. (Abstract shortened by UMI.)

The spatial distribution of the tremendous bacterial diversity in soil partially depends on the broad range of scales of soil physical structures and the size of bacteria. The aim of this article is to collect information on spatial distribution of bacteria, the genetic structure of bacterial populations and communities, and on spatial constraints that operate in soil. This has been addressed by studying the spatial pattern of micro-habitats for various bacterial types and the spatial spread of clones in soil environment. The clones were considered as the units of genetic population structure. Experimental findings from a number of studies provide evidence that in soils a clone and a micro-colony are not necessarily identical. For some bacterial types, members of the same clone have been found far apart. Besides, micro-colonies of a few cells have also been reported. Short-range cell movements seem to be common in soil, in agreement with the observation of high small-scale diversity (millimetre scale). The mechanisms for the spread of clones are complex and probably operate at different spatial scales, even for soil bacteria with no specific vectors. The hypothesis underlying the study of the spatial dimension of diversity is that it can reveal mechanisms of diversity maintenance and contribute to their evaluation, complementing available knowledge of genetic processes.

Altitude is the major factor affecting both biodiversity and soil physiochemical properties of soil ecosystems. In order to understand the effect of altitude on soil physiochemical properties and bacterial diversity across the Himalayan cold desert, high altitude Gangotri soil ecosystem was studied and compared with the moderate altitude Kandakhal soil. Soil physiochemical analysis showed that altitude was positively correlated with soil pH, organic matter and total nitrogen content. However soil mineral nutrients and soil phosphorus were negatively correlated to the altitude. RT-PCR based analysis revealed the decreased bacterial and diazotrophic abundance at high altitude. Metagenomic study showed that Proteobacteria, Acidobacteria and Actinobacteria were dominant bacteria phyla at high altitude soil while Bacteroidetes and Fermicutes were found dominant at low altitude. High ratio of Gram-negative to Gram positive bacteria at Gangotri suggests the selective proliferation of Gram negative bacteria at high altitude with decrease in Gram positive bacteria. Moreover, Alphaproteobacteria was found more abundant at high altitude while the opposite was true for Betaproteobacteria. Abundance of Cytophaga, Flavobacterium and Bacteroides (CFB) were also found comparatively high at high altitude. Presence of many taxonomically unclassified sequences in Gangotri soil indicates the presence of novel bacterial diversity at high altitude. Further, isolation of bacteria through indigenously designed diffusion chamber revealed the existence of bacteria which has been documented in unculturable study of WIH (Western Indian Himalaya) but never been cultivated from WIH. Nevertheless, diverse functional free-living psychrotrophic diazotrophs were isolated only from the high altitude Gangotri soil. Molecular characterization revealed them as Arthrobacter humicola, Brevibacillus invocatus, Pseudomonas mandelii and Pseudomonas helmanticensis. Thus, this study documented the bacterial and psychrophilic diazotrophic diversity at high altitude and is an effort for exploration of low temperature bacteria in agricultural productivity with the target for sustainable hill agriculture.

Soils harbour some of the most diverse microbiomes on Earth and are essential for both nutrient cycling and carbon storage. To understand soil functioning, it is necessary to model the global distribution patterns and functional gene repertoires of soil microorganisms, as well as the biotic and environmental associations between the diversity and structure of both bacterial and fungal soil communities 1 – 4 . Here we show, by leveraging metagenomics and metabarcoding of global topsoil samples (189 sites, 7,560 subsamples), that bacterial, but not fungal, genetic diversity is highest in temperate habitats and that microbial gene composition varies more strongly with environmental variables than with geographic distance. We demonstrate that fungi and bacteria show global niche differentiation that is associated with contrasting diversity responses to precipitation and soil pH. Furthermore, we provide evidence for strong bacterial–fungal antagonism, inferred from antibiotic-resistance genes, in topsoil and ocean habitats, indicating the substantial role of biotic interactions in shaping microbial communities. Our results suggest that both competition and environmental filtering affect the abundance, composition and encoded gene functions of bacterial and fungal communities, indicating that the relative contributions of these microorganisms to global nutrient cycling varies spatially. Metagenomic, chemical and biomass analyses of topsoil samples from around the world reveal spatial and environmental trends in microbial community composition and genetic diversity.