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Soil microorganisms play an important role in determining nutrient cycling. The integration of fish into rice fields can influence the diversity and structural composition of soil microbial communities. However, regarding the rice–fish co-culture (RF) farming system in Thailand, the study of the diversity and composition of soil microbes is still limited. Here, we aim to compare the microbial diversity, community composition, and functional structure of the bacterial communities between RF and rice monoculture (MC) farming systems and identify the environmental factors shaping bacterial community composition. Bacterial taxonomy was observed using 16s rRNA gene amplicon sequencing, and the functional structures of the bacterial communities were predicted based on their taxonomy and sequences. The results showed that soil organic carbon, total nitrogen (TN), organic matter, available phosphorous, and clay content were significantly higher in RF than in MC. The most dominant taxa across both paddy rice fields belonged to Actinobacteria, Chloroflexi, Proteobacteria, Acidobacteria, and Planctomycetes. The taxa Nitrosporae, Rokubacteria, GAL15, and Elusimicrobia were significantly different between both rice fields. At the genus level, Bacillus, Anaeromyxobacter, and HSB OF53-F07 were the predominant genera in both rice fields. The most abundant genus in MC was Anaeromyxobacter, whereas RF belonged to Bacillus. The community composition in MC was positively correlated with magnesium and sand content, while in RF was positively correlated with pH, TN, and clay content. Nitrogen fixation, aromatic compound degradation, and hydrocarbon degradation were more abundant in RF, while cellulolysis, nitrification, ureolysis, and phototrophy functional groups were more abundant in MC. The enzymes involved in paddy soil ecosystems included phosphatase, β-glucosidase, cellulase, and urease. These results provide novel insights into integrated fish in the paddy field as an efficient agricultural development strategy for enhancing soil microorganisms that increase soil fertility.

Patescibacteria are an enigmatic group of bacteria of ultra-small sizes and reduced genomes, commonly found in subsurface environments but largely unexplored in terms of their ecological roles. Despite being present in both freshwater and marine systems, no study has explored how they distribute along salinity gradients. This study provides new insights into their distribution, diversity, and niche partitioning along a Mediterranean subterranean estuary characterized by a strong salinity gradient. We show that Patescibacteria taxa seem to adapt to varying groundwater salinity conditions, displaying a remarkable capacity to occupy fresh, brackish, and saline niches through changes in composition. The identification of ultra-small coccoid cells and symbiotic-like associations highlights a diversity of lifestyles within these groups and provides one of the scarce visual proofs of Patescibacteria. With most detected taxa being highly novel, these findings point to an overlooked importance of Patescibacteria in coastal aquifers, biogeochemically active sites ubiquitous along most coastlines.

The ascomycetous fungus Nectria haematococca, (asexual name Fusarium solani), is a member of a group of >50 species known as the \"Fusarium solani species complex\". Members of this complex have diverse biological properties including the ability to cause disease on >100 genera of plants and opportunistic infections in humans. The current research analyzed the most extensively studied member of this complex, N. haematococca mating population VI (MPVI). Several genes controlling the ability of individual isolates of this species to colonize specific habitats are located on supernumerary chromosomes. Optical mapping revealed that the sequenced isolate has 17 chromosomes ranging from 530 kb to 6.52 Mb and that the physical size of the genome, 54.43 Mb, and the number of predicted genes, 15,707, are among the largest reported for ascomycetes. Two classes of genes have contributed to gene expansion: specific genes that are not found in other fungi including its closest sequenced relative, Fusarium graminearum; and genes that commonly occur as single copies in other fungi but are present as multiple copies in N. haematococca MPVI. Some of these additional genes appear to have resulted from gene duplication events, while others may have been acquired through horizontal gene transfer. The supernumerary nature of three chromosomes, 14, 15, and 17, was confirmed by their absence in pulsed field gel electrophoresis experiments of some isolates and by demonstrating that these isolates lacked chromosome-specific sequences found on the ends of these chromosomes. These supernumerary chromosomes contain more repeat sequences, are enriched in unique and duplicated genes, and have a lower G+C content in comparison to the other chromosomes. Although the origin(s) of the extra genes and the supernumerary chromosomes is not known, the gene expansion and its large genome size are consistent with this species' diverse range of habitats. Furthermore, the presence of unique genes on supernumerary chromosomes might account for individual isolates having different environmental niches

Here, we sought phages that were capable of infecting Patescibacteriota metagenome-assembled genomes (MAGs), and further explored the diversity and novelty of Patescibacteriota phages, as well as the mechanisms underlying phage-Patescibacteriota interactions in groundwater ecosystems. The abundance profiles of phage-Patescibacteriota interactions suggested that lysogenic infection may represent a mutually adapted strategy between Patescibacteriota and their phages in groundwater ecosystems. Furthermore, the groundwater Patescibacteriota phages possessed diverse auxiliary metabolic genes which might facilitate the symbiotic associations and metabolic exchange between host Patescibacteriota MAGs and other free-living microbes and expand the metabolic capabilities of host Patescibacteriota MAGs. This study elucidated the mechanisms of phage-Patescibacteriota interactions and the potential roles of phages in modulating the physiology and ecology of Patescibacteriota within groundwater ecosystems.

Rice straw and stubble burning is widely practiced to clear fields for new crops. However, questions remain about the effects of fire on soil bacterial communities and soil properties in paddy fields. Here, five adjacent farmed fields were investigated in central Thailand to assess changes in soil bacterial communities and soil properties after burning. Samples of soil prior to burning, immediately after burning, and 1 year after burning were obtained from depths of 0 to 5 cm. The results showed that the pH, electrical conductivity, NH4-N, total nitrogen, and soil nutrients (available P, K, Ca, and Mg) significantly increased immediately after burning due to an increased ash content in the soil, whereas NO3-N decreased significantly. However, these values returned to the initial values. Chloroflexi were the dominant bacteria, followed by Actinobacteria and Proteobacteria. At 1 year after burning, Chloroflexi abundance decreased remarkably, whereas Actinobacteria, Proteobacteria, Verrucomicrobia, and Gemmatimonadetes abundances significantly increased. Bacillus, HSB OF53-F07, Conexibacter, and Acidothermus abundances increased immediately after burning, but were lower 1 year after burning. These bacteria may be highly resistant to heat, but grow slowly. Anaeromyxobacter and Candidatus Udaeobacter dominated 1 year after burning, most likely because of their rapid growth and the fact that they occupy areas with increased soil nutrient levels after fires. Amidase, cellulase, and chitinase levels increased with increased organic matter levels, whereas β-glucosidase, chitinase, and urease levels positively correlated with the soil total nitrogen level. Although clay and soil moisture strongly correlated with the soil bacterial community’s composition, negative correlations were found for β-glucosidase, chitinase, and urease. In this study, rice straw and standing stubble were burnt under high soil moisture and within a very short time, suggesting that the fire was not severe enough to raise the soil temperature and change the soil microbial community immediately after burning. However, changes in soil properties due to ash significantly increased the diversity indices, which was noticeable 1 year after burning.

The ecological balance of an ecosystem has a relation to its biodiversity. Although it has been established that biodiversity and ecological stability are related, generalization about the exact nature of this relation remains elusive and more so in microbial diversity. A growing volume of studies has indicated that anthropogenic activities impact biodiversity, but it is difficult to generalize the impact of anthropogenic activities on microbial diversity. Landfilling by municipal solid waste is one such activity where microbes play a major role, and leachates are released from the landfill, altering the soil’s physical and chemical nature. Change in factors like carbon source, pH, and toxicity of the soil is most likely to affect the indigenous microflora of the soil. The present study was undertaken to compare the microbial diversity of soil receiving landfill leachate with that of the soil not receiving any landfill leachate to assess the impact of the landfilling activity on microbial diversity. The landfill site selected for the study was that of Kamrup Metro District of Assam, located at Boragaon, near the Ramsar wetland called Deeporbeel. By using the Denaturing Gradient Gel Electrophoresis (DGGE) method, it has been found that the microbial diversity of the soil receiving leachate was higher than that of the soil not receiving any leachate from the landfill.

Lactic Acid Bacteria Biodiversity and Taxonomy Lactic Acid Bacteria Biodiversity and Taxonomy Edited by Wilhelm H. Holzapfel and Brian J.B. Wood The lactic acid bacteria (LAB) are a group of related microorganisms that are enormously important in the food and beverage industries. Generally regarded as safe for human consumption (and, in the case of probiotics, positively beneficial to human health), the LAB have been used for centuries, and continue to be used worldwide on an industrial scale, in food fermentation processes, including yoghurt, cheeses, fermented meats and vegetables, where they ferment carbohydrates in the foods, producing lactic acid and creating an environment unsuitable for the survival of food spoilage organisms and pathogens. The shelf life of the product is thereby extended, but of course these foods are also enjoyed around the world for their organoleptic qualities. They are also important to the brewing and winemaking industries, where they are often undesirable intruders but can in specific cases have desirable benefits. The LAB are also used in producing silage and other agricultural animal feeds. Clinically, they can improve the digestive health of young animals, and also have human medical applications. This book provides a much-needed and comprehensive account of the current knowledge of the LAB, covering the taxonomy and relevant biochemistry, physiology and molecular biology of these scientifically and commercially important microorganisms. It is directed to bringing together the current understanding concerning the organisms' remarkable diversity within a seemingly rather constrained compass. The genera now identified as proper members of the LAB are treated in dedicated chapters, and the species properly recognized as members of each genus are listed with detailed descriptions of their principal characteristics. Each genus and species is described using a standardized format, and the relative importance of each species in food, agricultural and medical applications is assessed. In addition, certain other bacterial groups (such as Bifidobacterium) often associated with the LAB are given in-depth coverage. The book will also contribute to a better understanding and appreciation of the role of LA B in the various ecosystems and ecological niches that they occupy. In summary, this volume gathers together information designed to enable the organisms' fullest industrial, nutritional and medical applications. Lactic Acid Bacteria: Biodiversity and Taxonomy is an essential reference for research scientists, biochemists and microbiologists working in the food and fermentation industries and in research institutions. Advanced students of food science and technology will also find it an indispensable guide to the subject. Also available from Wiley Blackwell The Chemistry of Food Jan Velisek ISBN 978-1-118-38384-1 Progress in Food Preservation Edited by Rajeev Bhat, Abd Karim Alias and Gopinadham Paliyath ISBN 978-0-470-65585-6

This study investigates the potential of leaf and various organic waste composts as bio-organic fertilizers using 16S rRNA metagenomics. The microbial richness and diversity analysis, employing alpha and beta diversity indices, reveal substantial variations influenced by organic substrates during composting. The leaf compost had a high total OTU (70,554) but low microbial diversity (Chao 1 index = 272.27). The kitchen waste compost had the highest microbial diversity (Chao 1 index = 429.18). Positive correlations between microbial biomass, diversity, and compost quality highlighted the pivotal role of microbial activity. The beneficial genera identified across all the bio-composts were Lactobacillus, Leuconostoc, Sphingobacterium, Paenibacillus, Pseudomonas, and Clostridium. Some pathogenic genera were also detected in all the composts analyzed, viz. Prevotella, Agrobacterium, Fusobacterium, and Streptococcus. Nonetheless, the ratio of beneficial to the pathogenic genera was generally high in all compost, highlighting the enrichment with beneficial microorganisms. The leaf compost demonstrated the highest proportion of beneficial genera, about 92%, indicating significant bio-fertilizing potential, with a low % level of pathogenic genera of about 3%. Thus, the leaf compost has excellent potential to be used as a bio-organic fertilizer. Understanding the microbial composition of organic waste composts is crucial for its application as bio-fertilizer for promoting sustainable agriculture.

Despite recent great advances in microbial culture, most microbes have not yet been cultured, and the impact of medium composition on the isolation of microbes from natural systems has not been elucidated. To optimize media for culturing marine microbes, microbial communities in three sediment samples were described using high-throughput sequencing (HTS) and culture-dependent techniques. HTS revealed communities dominated by Gammaproteobacteria , and culture-based methods revealed communities dominated by Actinobacteria . Among the total operational taxonomic units (OTUs) from the HTS dataset, 6% were recovered in the culture collection. Four potentially novel bacterial strains belonging to Oceaniovalibus , Psychrobacter and Salegentibacter were isolated. The combination of media cultured more taxa than any single medium. Nutrient-rich and single-carbon/nitrogen-source media supported the growth of relatively few taxa, and the quality of nitrogen strongly influenced the types of bacteria isolated.

The effect of plant invasion on soil microbial communities in various ecosystems has increasingly become the focus of research over the last decade. Moso bamboo (Phyllostachys edulis) invasion of native forests in Tianmushan National Nature Reserve located in southeastern China has resulted in greatly decreased biodiversity of plants and birds. We combined three different microbial community techniques (Biolog, cellular fatty acids, and 16S-PCR–DGGE) to examine whether changes in the overstory of plant taxa, or any associated environmental changes, modified soil microbial communities. Three types of forests were examined: mono-bamboo forest, mixed forest of bamboo and broadleaf, and native broadleaf forest. The fatty acid and DGGE results showed that bamboo invasion of the native forest influenced soil community structure and increased microbial biomass and taxonomic diversity despite decreased plant diversity. The Biolog results indicated no change in microbial functional diversity as a result of bamboo invasion. Evidence from bacterial PCR–DGGE suggested that bamboo stimulated the growth of otherwise undetected soil bacterial species. Overall, the results indicate that bamboo invasion may significantly affect associated soil microbial communities.