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In an attempt to isolate new probiotic bacteria, two Gram-variable, spore-forming, rod-shaped aerobic bacteria designated as strain A4 and A15 were isolated from the feces of Canada geese (Branta canadensis). Strain A4 was able to grow in high salt levels and exhibited lipase activity, while A15 did not propagate under these conditions. Both were positive for starch hydrolysis, and they inhibited the growth of Staphylococcus aureus. The strains of the 16S rRNA sequence shared only 94% similarity to previously identified Sporosarcina spp. The ANI (78.08%) and AAI (82.35%) between the two strains were less than the species threshold. Searches for the most similar genomes using the Mash/Minhash algorithm showed the nearest genome to strain A4 and A15 as Sporosarcina sp. P13 (distance of 21%) and S. newyorkensis (distance of 17%), respectively. Sporosarcina spp. strains A4 and A15 contain urease genes, and a fibronectin-binding protein gene indicates that these bacteria may bind to eukaryotic cells in host gastrointestinal tracts. Phenotypic and phylogenetic data, along with low dDDH, ANI, and AAI values for strains A4 and A15, indicate these bacteria are two novel isolates of the Sporosarcina genus: Sporosarcina sp. A4 sp. nov., type strain as Sporosarcina cascadiensis and Sporosarcina sp. A15 sp. nov., type strain Sporosarcina obsidiansis. [ABSTRACT FROM AUTHOR]

Abstract Background Soils harbour high diversity of obligate as well as facultative chemolithoautotrophic bacteria that contribute significantly to CO2 dynamics in soil. In this study, we used culture dependent and independent methods to assess the community structure and diversity of chemolithoautotrophs in agricultural and coastal barren saline soils (low and high salinity). We studied the composition and distribution of chemolithoautotrophs by means of functional marker gene cbbL encoding large subunit of ribulose-1,5-bisphosphate carboxylase/oxygenase and a phylogenetic marker 16S rRNA gene. The cbbL form IA and IC genes associated with carbon fixation were analyzed to gain insight into metabolic potential of chemolithoautotrophs in three soil types of coastal ecosystems which had a very different salt load and sulphur content. Results In cbbL libraries, the cbbL form IA was retrieved only from high saline soil whereas form IC was found in all three soil types. The form IC cbbL was also amplified from bacterial isolates obtained from all soil types. A number of novel monophyletic lineages affiliated with form IA and IC phylogenetic trees were found. These were distantly related to the known cbbL sequences from agroecosystem, volcanic ashes and marine environments. In 16S rRNA clone libraries, the agricultural soil was dominated by chemolithoautotrophs (Betaproteobacteria) whereas photoautotrophic Chloroflexi and sulphide oxidizers dominated saline ecosystems. Environmental specificity was apparently visible at both higher taxonomic levels (phylum) and lower taxonomic levels (genus and species). The differentiation in community structure and diversity in three soil ecosystems was supported by LIBSHUFF (P = 0.001) and UniFrac. Conclusion This study may provide fundamentally new insights into the role of chemolithoautotrophic and photoautotrophic bacterial diversity in biochemical carbon cycling in barren saline soils. The bacterial communities varied greatly among the three sites, probably because of differences in salinity, carbon and sulphur contents. The cbbL form IA-containing sulphide-oxidizing chemolithotrophs were found only in high saline soil clone library, thus giving the indication of sulphide availability in this soil ecosystem. This is the first comparative study of the community structure and diversity of chemolithoautotrophic bacteria in coastal agricultural and saline barren soils using functional (cbbL) and phylogenetic (16S rDNA) marker genes.

The concept of successional trajectories describes how small differences in initial community composition can magnify through time and lead to significant differences in mature communities. For many animals, the types and sources of early-life exposures to microbes have been shown to have significant and long-lasting effects on the community structure and/or function of the microbiome. In modern commercial poultry production, chicks are reared as a single age cohort and do not directly encounter adult birds. This scenario is likely to initiate a trajectory of microbial community development that is significantly different than non-industrial settings where chicks are exposed to a much broader range of environmental and fecal inocula; however, the comparative effects of these two scenarios on microbiome development and function remain largely unknown. In this work, we performed serial transfers of cecal material through multiple generations of birds to first determine if serial transfers exploiting the ceca in vivo, rather than the external environment or artificial incubations, can produce a stable microbial community. Subsequently, we compared microbiome development between chicks receiving this passaged, i.e. host-selected, cecal material orally, versus an environmental inoculum, to test the hypothesis that the first exposure of newly hatched chicks to microbes determines early GI microbiome structure and may have longer-lasting effects on bird health and development. Cecal microbiome dynamics and bird weights were tracked for a two-week period, with half of the birds in each treatment group exposed to a pathogen challenge at 7 days of age. We report that: i) a relatively stable community was derived after a single passage of transplanted cecal material, ii) this cecal inoculum significantly but ephemerally altered community structure relative to the environmental inoculum and PBS controls, and iii) either microbiome transplant administered at day-of-hatch appeared to have some protective effects against pathogen challenge relative to uninoculated controls. Differentially abundant taxa identified across treatment types may inform future studies aimed at identifying strains associated with beneficial phenotypes. [ABSTRACT FROM AUTHOR]

Knowledge regarding bacterial dynamics during crop ensiling is important for understanding of the fermentation process and may facilitate the production of nutritious and stable silage. The objective of this study was to analyze the bacterial dynamics associated with whole crop wheat silage with and without inoculants. Whole crop wheat was ensiled in laboratory silos, with and without Lactobacillus inoculants (L. plantarum, L. buchneri), for 3 months. Untreated and L. plantarum -treated silages were sampled at several times during ensiling, while L. buchneri -treated silage was sampled only at 3 months. Bacterial composition was studied using next generation sequencing approach. Dominant bacteria, before ensiling, were Pantoea (34.7%), Weissella (28.4%) and Pseudomonas (10.4%), Exiguobacterium (7.8%), and Paenibacillus (3.4%). Exogenous inoculants significantly affected bacterial composition and dynamics during ensiling. At 3 months of ensiling, Lactobacillus dominated the silage bacterial population and reached an abundance of 59.5, 92.5, and 98.2% in untreated, L. plantarum - and L. buchneri -treated silages, respectively. The bacterial diversity of the mature silage was lower in both treated silages compared to untreated silage. Functional profiling of the bacterial communities associated with the wheat ensiling demonstrated that the abundant pathways of membrane transporters, carbohydrate and amino acids metabolisms followed different pattern of relative abundance in untreated and L. plantarum -treated silages. Only three pathways, namely base-excision repair, pyruvate metabolism and transcription machinery, were significantly different between untreated and L. buchneri -treated silages upon maturation. Lactic acid content was higher in L. plantarum- treated silage compared to untreated and L. buchneri- treated silage. Still, the pH of both treated silages was lower in the two Lactobacillus -treated silages compared to untreated silage. Aerobic stability test demonstrated that L. plantarum -, but not L. buchneri -supplement, facilitated silage deterioration. The lower aerobic stability of the L. plantarum -treated silage may be attributed to lower content of acetic acid and other volatile fatty acids which inhibit aerobic yeasts and molds. Indeed, high yeast count was recorded, following exposure to air, only in L. plantarum -treated silage, supporting this notion. Analysis of bacterial community of crop silage can be used for optimization of the ensiling process and the selection of appropriate inoculants for improving aerobic stability. [ABSTRACT FROM AUTHOR]

Microbial population dynamics associated with corn silage, with and without Lactobacillus plantarum treatment, was studied. Whole crop corn was ensiled using laboratory silos and sampled at different times, up to 3 months. The dominant bacteria, before ensiling, were Acinetobacter (38.5%) and Klebsiella (16.3%), while the dominant fungi were Meyerozyma (53.5%) and Candida (27.7%). During ensiling, the microbial population shifted considerably, and Lactobacillus (> 94%) and Candida (> 74%) became the most dominant microbial genera in both treated and untreated silages. Yet, lactic acid content was higher in the treated silage, while the microbial diversity was lower than in the untreated silage. Upon aerobic exposure, spoilage occurred more rapidly in the treated silage, possibly due to the higher abundance of lactic acid-assimilating fungi, such as Candida. Our study is the first to describe microbial population dynamics during whole-crop corn ensiling and the results indicate that microbial diversity may be an indicator of aerobic stability. [ABSTRACT FROM AUTHOR]

The Gulf of Cambay is a trumpet-shaped inlet of the Arabian Sea, located along the west coast of India and confronts a high tidal range with strong water currents. The region belongs to a semi-arid zone and saline alkaline intertidal soils are considered biologically extreme. The selected four soil types (S1–S4) were affected by salinity, alkalinity and sodicity. Soil salinity ranged from 20 to 126 dS/m, soil pH 8.6–10.0 with high sodium adsorption ratio (SAR) and exchangeable sodium percentage (ESP). Abundance of the key functional genes like cbbL , nifH , amoA and apsA involved in biogeochemical cycling were targeted using qPCR, which varied from (2.36 ± 0.03) × 10 4 to (2.87 ± 0.26) × 10 8 , (1.18 ± 0.28) × 10 6 to (1.01 ± 0.26) × 10 9 , (1.41 ± 0.21) × 10 6 to (1.29 ± 0.05) × 10 8 and (8.47 ± 0.23) × 10 4 to (1.73 ± 0.01) × 10 6 per gram dry weight, respectively. The microbial community structure revealed that soils S1 and S3 were dominated by phylum Firmicutes whereas S4 and S2 showed an abundance of Proteobacterial clones. These soils also represented Bacteroidetes, Chloroflexi, Actinobacteria, Planctomycetes and Acidobacteria clones. Molecular phylogeny showed a significant variation in the bacterial community distribution among the intertidal soil types. A high number of novel taxonomic units were observed which makes the intertidal zone a unique reservoir of unidentified bacterial taxa that may be explored further. [ABSTRACT FROM AUTHOR]

A metagenomic approach was applied using 454-pyrosequencing data analysis for the profiling of bacterial communities in the brine samples of the water reclamation plant. Some physicochemical characteristics of brine samples were also determined using standard methods. Samples ranged from being lightly alkaline to highly alkaline (pH 7.40-10.91) throughout the various treatment stages, with the salinity ranging from 1.62 to 4.53 g L−1 and dissolved oxygen concentrations ranging from 7.47 to 9.12 mg L−1. Phenotypic switching was found to occur due to these physicochemical parameters. Microbial diversities increased from those present in Stage I reactor (six taxonomic groups) to those in Reverse Osmosis (RO) stage I (17 taxonomic groups), whereas in the second phase of the treatment, it increased in Stage II clarifier (14 taxonomic groups) followed by a decrease in RO stage II (seven taxonomic groups). Overall, seven phyla were detected, apart from many bacterial sequences that were unclassified at the phylum level. The most dominant phylum found was Proteobacteria accounting for 59% of the total sequences. A blastn sequence similarity search showed that the majority of the sequences (56%) were homologous to the uncultured bacterial species, underlining the vast untapped bacterial diversity. [ABSTRACT FROM AUTHOR]

Highlights: [•] Evaluation of substrates for bioremediation of ATIE by an alkaliphile. [•] The isolate, capable to bring down the pH of effluent from 12.0 to 7.0 within 2h. [•] SB and MI promising for neutralization and biosorption of dyes from the ATIE. [•] Carboxylic acid produced facilitated neutralization of effluent revealed by FTIR and NMR analysis. [•] Neutralization of effluents could be a viable, economic and eco-friendly process. [ABSTRACT FROM AUTHOR]

Bacterial community structures in two physicochemically different soils from the coastal region of Gujarat, India were investigated using PCR, 16S rRNA gene clone libraries and sequencing methods. The aim of the study was to determine the diversity of bacterial communities inhabiting haloalkaline soil from a semi-arid coastal region. The phylogenetic diversity of bacteria in a haloalkaline soil (EC 20 dS/m; pH 9.5) was compared with a normal soil (EC 0.93 dS/m; pH 7.2). Clones representing phylaProteobacteria,Bacteroidetes,Chloroflexi,Firmicutes,Actinobacteria,AcidobacteriaandPlanctomyceteswere found in both soils.Cyanobacteria,Verrucomicrobia,OP10andBacteria incertae sediswere detected in normal soil whereasNitrospirawas found only in haloalkaline soil. The dominant phylum in the haloalkaline soil wasBacteroidetesfollowed byProteobacteriawhereas normal soil was dominated byProteobacteriaandActinobacteria. About 82% of the sequences from the haloalkaline library were related to those previously retrieved from various saline, alkaline and oil-natural gas field ecosystems whereas 50% of the sequences from normal soil resembled sequences of bacteria retrieved from agriculture-related habitats viz. agriculture fields, rhizosphere and grasslands. One third of the total sequences from both soil samples showed low BLAST identities (<95%) suggesting that these soils may harbor unique, novel taxa. Further, the correlation analysis revealed negative correlations of Shannon diversity indices and species evenness with salinity (EC) and pH but positive correlations with total carbon and total nitrogen contents of the soil samples. The haloalkaline soil exhibited less bacterial diversity and communities were significantly different from those of normal soil. In this study, the haloalkaline soil from a semi-arid region supports oligotrophic microbes. Supplemental materials are available for this article. Go to the publisher's online edition ofGeomicrobiology Journalto view the supplemental file. [ABSTRACT FROM PUBLISHER]

Abstract: Population indices of bacteria and archaea were investigated from saline–alkaline soil and a possible microbe–environment pattern was established using gene targeted metagenomics. Clone libraries were constructed using 16S rRNA and functional gene(s) involved in carbon fixation (cbbL), nitrogen fixation (nifH), ammonia oxidation (amoA) and sulfur metabolism (apsA). Molecular phylogeny revealed the dominance of Actinobacteria, Firmicutes and Proteobacteria along with archaeal members of Halobacteraceae. The library consisted of novel bacterial (20%) and archaeal (38%) genera showing ≤95% similarity to previously retrieved sequences. Phylogenetic analysis indicated ability of inhabitant to survive in stress condition. The 16S rRNA gene libraries contained novel gene sequences and were distantly homologous with cultured bacteria. Functional gene libraries were found unique and most of the clones were distantly related to Proteobacteria, while clones of nifH gene library also showed homology with Cyanobacteria and Firmicutes. Quantitative real-time PCR exhibited that bacterial abundance was two orders of magnitude higher than archaeal. The gene(s) quantification indicated the size of the functional guilds harboring relevant key genes. The study provides insights on microbial ecology and different metabolic interactions occurring in saline–alkaline soil, possessing phylogenetically diverse groups of bacteria and archaea, which may be explored further for gene cataloging and metabolic profiling. [Copyright &y& Elsevier]

Abstract: Sequestration of CO2 by autotrophic bacteria is a key process of biogeochemical carbon cycling in soil ecosystem. Rhizosphere is a rich niche of microbial activity and diversity, influenced by change in atmospheric CO2. Structural changes in rhizosphere composition influence microbial communities and the nutrient cycling. In the present study, the bacterial diversity and population dynamics were established using cbbL and 16S rRNA gene targeted metagenomics approach from the rhizosphere of Arachis hypogaea. A total of 108 cbbL clones were obtained from the rhizospheric soil which revealed predominance of cbbL sequences affiliated to Rhizobium leguminosarum, Bradyrhizobium sp., Sinorhizobium meliloti, Ochrobactrum anthropi and a variety of uncultured cbbL harboring bacteria. The 16S rRNA gene clone library exhibited the dominance of Firmicutes (34.4%), Proteobacteria (18.3%), Actinobacteria (17.2%) and Bacteroidetes (16.1%). About 43% nucleotide sequences of 16S rRNA gene clone library were novel genera which showed <95% homology with published sequences. Gene copy number of cbbL and 16S rRNA genes, determined by quantitative real‐time PCR (qRT PCR), was 9.38±0.75×107 and 5.43±0.79×108 (per g dry soil), respectively. The results exhibited bacterial community structure with high bacterial diversity and abundance of CO2‐fixing bacteria, which can be explored further for their role in carbon cycling, sustainable agriculture and environment management. [Copyright &y& Elsevier]

Sprouts are considered a healthy ready-to-eat food and has gained popularity in recent years. The objective of the present study was to determine the dynamics of sprouts' microbiome during cold storage to the end of their shelf-life at home. The microbiological quality of fresh alfalfa (Medicago sativa) and mung bean (Vigna radiata) sprouts from two commercial brands was tested and the number of APC ranges from 5.0 to 8.7 log CFU/g in alfalfa and 6.7 to 9.3 log CFU/g in mung bean sprouts. In the case of alfalfa, but not mung beans, there were differences in the mean numbers of APC between the two brands. The number of coliform bacteria ranges from 4.3 to 7.7 log CFU/g in alfalfa and 4.1 to 8.1 log CFU/g in mung bean sprouts. Four independent batches of sprouts were used for DNA preparation and were sampled immediately after purchase and once a week during subsequent storage in refrigerator until the end of their shelf-life. Microbial population of the sprouts was determined using next generation sequencing of 16S rRNA amplicons. Alfalfa sprouts were dominated by Pseudomonas throughout the storage time with relative abundance of >60% at 3 weeks. Fresh mung bean sprouts were dominated by both Pseudomonas and Pantoea, but Pantoea became the dominant taxa after 2 weeks of storage, with >46% of relative abundance. The bacterial communities associated with sprouts were largely dependent on the sprout type, and less dependent on the brand. The species richness and diversity declined during storage and the development of spoilage. Among the 160 genera identified on sprouts, 23 were reported to contain known spoilage-associated species and 30 genera comprise potential human pathogenic species. This study provides new insight into the microbiome dynamics of alfalfa and mung bean sprouts during cold storage. • A survey of commercial sprouts found that none contained Salmonella spp. or Listeria monocytogenes. • Microbiome dynamics of sprouts under cold storage is described for the first time. • Bacterial community composition is dependent on sprout's type, but not on brand. • Pseudomonas dominates alfalfa, while Pantoea dominate mung bean sprouts. • Diversity and richness of the sprouts' microbiomes deceased during cold storage. [ABSTRACT FROM AUTHOR]

Water quality is an important public health issue given that the presence of pathogenic organisms in such waters can adversely affect human and animal health. Despite the numerous studies conducted to assess the quality of environmental waters in many countries, limited efforts have been put on investigating the microbial quality of the sediments in developing countries and how this relates to different land uses. The present study evaluated the bacterial diversity in water and sediments in a highly used South African river to find out how the different land uses influenced the bacterial diversity, and to verify the human diseases functional classes of the bacterial populations. Samples were collected on river stretches influenced by an informal, a peri-urban and a rural settlement. Genomic DNA was extracted from water and sediment samples and sequenced on an Illumina® MiSeq platform targeting the 16S rRNA gene variable region V3-V4 from the genomic DNA. Metagenomic data analysis revealed that there was a great diversity in the microbial populations associated with the different land uses, with the informal settlement having the most considerable influence on the bacterial diversity in the water and sediments of the Apies River. The Proteobacteria (69.8%), Cyanobacteria (4.3%), Bacteroidetes (2.7%), and Actinobacteria (2.7%) were the most abundant phyla; the Alphaproteobacteria, Betaproteobacteria and Anaerolineae were the most recorded classes. Also, the sediments had a greater diversity and abundance in bacterial population than the water column. The functional profiles of the bacterial populations revealed an association with many human diseases including cancer pathways. Further studies that would isolate these potentially pathogenic organisms in the aquatic environment are therefore needed as this would help in protecting the lives of communities using such rivers, especially against emerging bacterial pathogens. [ABSTRACT FROM AUTHOR]

In an attempt to isolate new probiotic bacteria, two Gram-variable, spore-forming, rod-shaped aerobic bacteria designated as strain A4 and A15 were isolated from the feces of Canada geese ( Branta canadensis ). Strain A4 was able to grow in high salt levels and exhibited lipase activity, while A15 did not propagate under these conditions. Both were positive for starch hydrolysis, and they inhibited the growth of Staphylococcus aureus . The strains of the 16S rRNA sequence shared only 94% similarity to previously identified Sporosarcina spp. The ANI (78.08%) and AAI (82.35%) between the two strains were less than the species threshold. Searches for the most similar genomes using the Mash/Minhash algorithm showed the nearest genome to strain A4 and A15 as Sporosarcina sp. P13 (distance of 21%) and S. newyorkensis (distance of 17%), respectively. Sporosarcina spp. strains A4 and A15 contain urease genes, and a fibronectin-binding protein gene indicates that these bacteria may bind to eukaryotic cells in host gastrointestinal tracts. Phenotypic and phylogenetic data, along with low dDDH, ANI, and AAI values for strains A4 and A15, indicate these bacteria are two novel isolates of the Sporosarcina genus: Sporosarcina sp. A4 sp. nov., type strain as Sporosarcina cascadiensis and Sporosarcina sp. A15 sp. nov., type strain Sporosarcina obsidiansis .

In chickens, early life exposure to environmental microbes has long-lasting impacts on gastrointestinal (GI) microbiome development and host health and growth, via mechanisms that remain uncharacterized. In this study, we demonstrated that administrating a fecal microbiome transplant (FMT) from adults to day-of-hatch chicks results in significantly higher body mass of birds and decreased residual feed intake (RFI), implying enhanced feed efficiency, at 6 weeks of age. To assess the potential mechanisms through which FMT affects adult bird phenotype, we combined 16 S rRNA gene amplification, metagenomic, and comparative genomic approaches to survey the composition and predicted activities of the resident microbiome of various GI tract segments. Early life FMT exposure had a long-lasting significant effect on the microbial community composition and function of the ceca but not on other GI segments. Within the ceca of 6-week-old FMT birds, hydrogenotrophic microbial lineages and genes were most differentially enriched. The results suggest that thermodynamic regulation in the cecum, in this case via hydrogenotrophic methanogenic and sulfur-cycling lineages, potentially serving as hydrogen sinks, may enhance fermentative efficiency and dietary energy harvest capacity. Our study provides a specific mechanism of action through which early-life microbiome transplants modulate market-relevant phenotypes in poultry and, thereby, may represent a significant advance toward microbiome-focused sustainable agriculture., Competing Interests: The authors declare that the research was conducted in the absence of any commercial or financial relationships that could be construed as a potential conflict of interest., (Copyright © 2022 Ramírez, Keshri, Vahrson, Garber, Berrang, Cox, González-Cerón, Aggrey and Oakley.)

Here, we announce the draft genome sequences of two Clostridium strains, C8-1-8 and C2-6-12, isolated from the cecal contents of commercial broiler chickens (in Athens, GA). These strains may represent potentially novel species within the genus Clostridium , and these draft genomes allow further investigation into potential probiotics for poultry., (Copyright © 2020 Keshri et al.)

Here, we present the draft genome sequences of two Bacillus strains, HF117&#95;J1&#95;D and USDA818B3&#95;A, isolated in Pomona, California, from the gastrointestinal (GI) tract of backyard and commercial broiler chickens, respectively. The draft genomes of both strains appear to represent novel species., (Copyright © 2020 Keshri et al.)

Here, we present the draft genome sequences of two Paenibacillus strains, An7 and USDA918EY, isolated from goose feces (Bend, OR, USA) and chicken ceca (Pomona, CA, USA), respectively. These data may assist with analyses of microorganisms associated with free-ranging and commercial avian species., (Copyright © 2020 Keshri et al.)

Sequestration of CO(2) by autotrophic bacteria is a key process of biogeochemical carbon cycling in soil ecosystem. Rhizosphere is a rich niche of microbial activity and diversity, influenced by change in atmospheric CO(2). Structural changes in rhizosphere composition influence microbial communities and the nutrient cycling. In the present study, the bacterial diversity and population dynamics were established using cbbL and 16S rRNA gene targeted metagenomics approach from the rhizosphere of Arachis hypogaea. A total of 108 cbbL clones were obtained from the rhizospheric soil which revealed predominance of cbbL sequences affiliated to Rhizobium leguminosarum, Bradyrhizobium sp., Sinorhizobium meliloti, Ochrobactrum anthropi and a variety of uncultured cbbL harboring bacteria. The 16S rRNA gene clone library exhibited the dominance of Firmicutes (34.4%), Proteobacteria (18.3%), Actinobacteria (17.2%) and Bacteroidetes (16.1%). About 43% nucleotide sequences of 16S rRNA gene clone library were novel genera which showed <95% homology with published sequences. Gene copy number of cbbL and 16S rRNA genes, determined by quantitative real-time PCR (qRT PCR), was 9.38 ± 0.75 × 10(7) and 5.43 ± 0.79 × 10(8) (per g dry soil), respectively. The results exhibited bacterial community structure with high bacterial diversity and abundance of CO(2)-fixing bacteria, which can be explored further for their role in carbon cycling, sustainable agriculture and environment management., (Copyright © 2012 Elsevier B.V. All rights reserved.)