-
The Science of the Total Environment Nov 2023Coastal wetlands are undergoing substantial transformations globally as a result of increased human activities. However, compared to other ecosystems, diversity and...
Coastal wetlands are undergoing substantial transformations globally as a result of increased human activities. However, compared to other ecosystems, diversity and functional characteristics of microbial communities in reclaimed coastal wetlands are not well studied compared to other ecosystems. This is important because it is known that microorganisms can play a crucial role in biogeochemical cycling within coastal wetland ecosystems. Hence, this study utilized the high-throughput sequencing technique to investigate the structure and assembly processes of microbial communities in reclaimed coastal wetlands. The results revealed a substantial change in soil properties following coastal wetland reclamation. Remarkably, the reclaimed soil exhibited significantly lower pH, soil organic carbon (SOC), and total salinity (TS) values (p < 0.05). The dominant phyla included Proteobacteria, Chloroflexi, Bacteroidetes, Acidobacteria, and Planctomycetes among study sites. However, the relative abundance of Proteobacteria increased from un-reclaimed coastal wetlands to reclaimed ones. The Proteobacteria, Chloroflexi, and Acidobacteria showed higher relative abundance in vegetated soil compared to bare soil, while Bacteroidetes and Planctomycetes exhibited the opposite trend. Notably, vegetation types exerted the strongest influence on microbial diversity, surpassing the effects of soil types and depth (F = 34.49, p < 0.001; F = 25.49, p < 0.001; F = 3.173, p < 0.078, respectively). Stochastic assembly processes dominated in un-reclaimed soil, whereas deterministic processes governed the assembly in artificial sea embankment wetlands (SEW). The presence of Spartina alterniflora in all soil types (except SEW soils) indicated stochastic assembly, while Phragmites australis in reclaimed soils pointed toward deterministic microbial assembly. Furthermore, environmental factors such as pH, soil water content (SWC), SOC, total carbon (TC), total nitrogen (TN), total phosphorus (TP), NH-N, vegetation types, soil depth, and geographic distance exhibited significant effects on microbial beta diversity indices. Co-occurrence network analysis revealed a stronger association between taxa in SEW compared to land reclaimed from wetlands (LRW) and natural coastal wetlands (NCW). The bottom soil layer exhibited more complex network interactions than the topsoil layer. Besides soil parameters, reclamation and varieties of vegetation were also substantial factors influencing the composition, diversity, and assembly processes of microbial communities in coastal wetlands.
Topics: Humans; Wetlands; Ecosystem; Soil; Carbon; Poaceae; Proteobacteria; Acidobacteria; Bacteroidetes; China
PubMed: 37567310
DOI: 10.1016/j.scitotenv.2023.166190 -
Current Opinion in Microbiology Jun 2024The governing principles and suites of genes for lateral elongation or incorporation of new cell wall material along the length of a rod-shaped cell are well described.... (Review)
Review
The governing principles and suites of genes for lateral elongation or incorporation of new cell wall material along the length of a rod-shaped cell are well described. In contrast, relatively little is known about unipolar elongation or incorporation of peptidoglycan at one end of the rod. Recent work in three related model systems of unipolar growth (Agrobacterium tumefaciens, Brucella abortus, and Sinorhizobium meliloti) has clearly established that unipolar growth in the Hyphomicrobiales order relies on a set of genes distinct from the canonical elongasome. Polar incorporation of envelope components relies on homologous proteins shared by the Hyphomicrobiales, reviewed here. Ongoing and future work will reveal how unipolar growth is integrated into the alphaproteobacterial cell cycle and coordinated with other processes such as chromosome segregation and cell division.
Topics: Brucella abortus; Sinorhizobium meliloti; Bacterial Proteins; Agrobacterium tumefaciens; Cell Wall; Peptidoglycan; Cell Division
PubMed: 38569420
DOI: 10.1016/j.mib.2024.102470 -
MSystems Dec 2023Antimicrobial resistance (AMR) has become a significant global challenge, with an estimated 10 million deaths annually by 2050. The emergence of AMR is mainly attributed...
Antimicrobial resistance (AMR) has become a significant global challenge, with an estimated 10 million deaths annually by 2050. The emergence of AMR is mainly attributed to mobile genetic elements (MGEs or mobilomes), which accelerate wide dissemination among pathogens. The interaction between mobilomes and AMR genes (or resistomes) in , a primary cause of diarrheal diseases that results in over 90 million cases annually, remains poorly understood. The available fragmented or incomplete genomes remain a significant limitation in investigating the relationship between AMR and MGEs. Here, we collected the most extensive closed genomes ( = 1,817) from various sources across 58 countries. Notably, our results demonstrate that resistome transmission between lineages follows a specific pattern of MGEs and is influenced by external drivers, including certain socioeconomic factors. Therefore, targeted interventions are urgently needed to mitigate the catastrophic consequences of AMR.
Topics: Salmonella; Drug Resistance, Bacterial
PubMed: 37855620
DOI: 10.1128/msystems.00883-23 -
Cell Reports Feb 2024Under stress conditions, translationally stalled mRNA and associated proteins undergo liquid-liquid phase separation and condense into cytoplasmic foci called stress...
Under stress conditions, translationally stalled mRNA and associated proteins undergo liquid-liquid phase separation and condense into cytoplasmic foci called stress granules (SGs). Many viruses hijack SGs for their pathogenesis; however, whether pathogenic bacteria also exploit this pathway remains unknown. Here, we report that members of the OspC family of Shigella flexneri induce SG formation in infected cells. Mechanistically, the OspC effectors target multiple subunits of the host translation initiation factor 3 complex by ADP-riboxanation. The modification of eIF3 leads to translational arrest and thus the formation of SGs. Furthermore, OspC-mediated SGs are beneficial for S. flexneri replication within infected host cells, and bacterial strains unable to induce SGs are attenuated for virulence in a murine model of infection. Our findings reveal a mechanism by which bacterial pathogens induce SG assembly by inactivating host translational machinery and promote bacterial proliferation in host cells.
Topics: Animals; Mice; Eukaryotic Initiation Factor-3; Stress Granules; Cytoplasm; Shigella; Shigella flexneri
PubMed: 38368608
DOI: 10.1016/j.celrep.2024.113789 -
PeerJ 2023Alkaline lakes are a special aquatic ecosystem that act as important water and alkali resource in the arid-semiarid regions. The primary aim of the study is to explore...
Alkaline lakes are a special aquatic ecosystem that act as important water and alkali resource in the arid-semiarid regions. The primary aim of the study is to explore how environmental factors affect community diversity and structure, and to find whether there are key microbes that can indicate changes in environmental factors in alkaline lakes. Therefore, four sediment samples (S1, S2, S3, and S4) were collected from Hamatai Lake which is an important alkali resource in Ordos' desert plateau of Inner Mongolia. Samples were collected along the salinity and alkalinity gradients and bacterial community compositions were investigated by Illumina Miseq sequencing. The results revealed that the diversity and richness of bacterial community decreased with increasing alkalinity (pH) and salinity, and bacterial community structure was obviously different for the relatively light alkaline and hyposaline samples (LAHO; pH < 8.5; salinity < 20‰) and high alkaline and hypersaline samples (HAHR; pH > 8.5; salinity > 20‰). Firmicutes, Proteobacteria and Bacteriodetes were observed to be the dominant phyla. Furthermore, Acidobacteria, Actinobacteria, and low salt-tolerant alkaliphilic nitrifying taxa were mainly distributed in S1 with LAHO characteristic. Firmicutes, Clostridia, Gammaproteobacteria, salt-tolerant alkaliphilic denitrifying taxa, haloalkaliphilic sulfur cycling taxa were mainly distributed in S2, S3 and S4, and were well adapted to haloalkaline conditions. Correlation analysis revealed that the community diversity (operational taxonomic unit numbers and/or Shannon index) and richness (Chao1) were significantly positively correlated with ammonium nitrogen (r = 0.654, < 0.05; r = 0.680, < 0.05) and negatively correlated with pH (r = -0.924, < 0.01; r = -0.800, < 0.01; r = -0.933, < 0.01) and salinity (r = -0.615, < 0.05; r = -0.647, < 0.05). A redundancy analysis and variation partitioning analysis revealed that pH (explanation degrees of 53.5%, pseudo-F = 11.5, < 0.01), TOC/TN (24.8%, pseudo-F = 10.3, < 0.05) and salinity (9.2%, pseudo-F = 9.5, < 0.05) were the most significant factors that caused the variations in bacterial community structure. The results suggested that alkalinity, nutrient salt and salinity jointly affect bacterial diversity and community structure, in which one taxon (Acidobacteria), six taxa (Cyanobacteria, Nitrosomonadaceae, , , and ) and five taxa (, , , and ) are related to carbon, nitrogen and sulfur cycles, respectively. Classes Clostridia and Gammaproteobacteria might indicate changes of saline-alkali conditions in the sediments of alkaline lakes in desert plateau.
Topics: Lakes; Ecosystem; Bacteria; Firmicutes; Acidobacteria; China; Alkalies; Ectothiorhodospiraceae
PubMed: 37637159
DOI: 10.7717/peerj.15909 -
Microbial Ecology Nov 2023Soil microorganisms play important roles in vegetation establishment and soil biogeochemical cycling. Ammodendron bifolium is a dominant sand-fixing (i.e., stabilizing...
The Composition and Diversity of the Rhizosphere Bacterial Community of Ammodendron bifolium Growing in the Takeermohuer Desert Are Different from Those in the Nonrhizosphere.
Soil microorganisms play important roles in vegetation establishment and soil biogeochemical cycling. Ammodendron bifolium is a dominant sand-fixing (i.e., stabilizing sand dunes) and endangered plant in the Takeermohuer Desert, and the bacterial community associated with this plant rhizosphere is still unclear. In this study, we investigated the composition and diversity of the bacterial community from the A. bifolium rhizosphere and bulk soil at different soil depths (i.e., 0-40 cm, 40-80 cm, 80-120 cm) using culture and high-throughput sequencing methods. We preliminarily analyzed the edaphic factors influencing the structure of bacterial communities. The results showed that the high-salinity Takeermohuer Desert has an oligotrophic environment, while the A. bifolium rhizosphere exhibited a relatively nutrient-rich environment due to higher contents of soil organic matter (SOM) and soil alkaline nitrogen (SAN) than bulk soil. The dominant bacterial groups in the desert were Actinobacteria (39.8%), Proteobacteria (17.4%), Acidobacteria (10.2%), Bacteroidetes (6.3%), Firmicutes (6.3%), Chloroflexi (5.6%), and Planctomycetes (5.0%) at the phylum level. However, the relative abundances of Proteobacteria (20.2%) and Planctomycetes (6.1%) were higher in the rhizosphere, and those of Firmicutes (9.8%) and Chloroflexi (6.9%) were relatively higher in barren bulk soil. A large number of Actinobacteria were detected in all soil samples, of which the most abundant genera were Streptomyces (5.4%) and Actinomadura (8.2%) in the bulk soil and rhizosphere, respectively. The Chao1 and PD_whole_tree indices in the rhizosphere soil were significantly higher than those in the bulk soil at the same soil depth and tended to decrease with increasing soil depth. Co-occurrence network analyses showed that the keystone species in the Takeermohuer Desert were the phyla Actinobacteria, Acidobacteria, Proteobacteria, and Chloroflexi. Furthermore, the major edaphic factors affecting the rhizosphere bacterial community were electrical conductivity (EC), SOM, soil total nitrogen (STN), SAN, and soil available potassium (SAK), while the major edaphic factors affecting the bacterial community in bulk soil were distance and ratio of carbon to nitrogen (C/N). We concluded that the A. bifolium rhizosphere bacterial community is different from that of the nonrhizosphere in composition, structure, diversity, and driving factors, which may improve our understanding of the relationship between plant and bacterial communities and lay a theoretical foundation for A. bifolium species conservation in desert ecosystems.
Topics: Ecosystem; Rhizosphere; Bacteria; Proteobacteria; Acidobacteria; Fabaceae; Soil; Plants; Nitrogen; Soil Microbiology
PubMed: 38008827
DOI: 10.1007/s00248-023-02320-9 -
Nature Reviews. Microbiology Mar 2024
Topics: Bdellovibrio bacteriovorus; Bacterial Proteins; Escherichia coli
PubMed: 38243075
DOI: 10.1038/s41579-024-01012-6 -
Acta Tropica Jul 2024This research offers a comprehensive exploration of the microbial communities associated with vector mosquitoes from South Korea. Aedes albopictus, Anopheles sinensis,...
This research offers a comprehensive exploration of the microbial communities associated with vector mosquitoes from South Korea. Aedes albopictus, Anopheles sinensis, and Culex molestus are vectors of pathogens, and understanding the intricacies of their microbiome profile is paramount for unraveling their roles in disease transmission dynamics. In this study, we characterized the microbiome of the midguts of adult female vector mosquitoes collected from different locations in South Korea. After DNA extraction from dissected mosquito midguts, we used the Illumina MiSeq next-generation sequencing to obtain sequences spanning the V4 hypervariable region of the bacteria 16S rRNA. Morphological and molecular characterization using 506-bp mitochondrial 16S rRNA was used to identify the mosquito species before amplicon sequencing. Across the three vector mosquitoes surveyed, 21 bacteria genera belonging to 20 families and 5 phyla were discovered. Proteobacteria and Bacteriodota were the major phyla of bacteria associated with the three mosquito species. There were significant differences in the gut microbiome genera composition between the species and little variation in the gut microbiome between individuals of the same mosquito species. Wolbachia is the most dominant genus in Aedes while Aeromonas, Acinetobacter, and unassigned taxa are the most common in An. sinensis. In addition to that, Chromobacterium, Chryseobacterium, and Aeromonas are dominant in Cx. molestus. This study sheds light on the complex interactions between mosquitoes and their microbiome, revealing potential implications for vector competence, disease transmission, and vector control strategies.
Topics: Animals; Republic of Korea; RNA, Ribosomal, 16S; Aedes; Mosquito Vectors; Bacteria; Female; Culex; Anopheles; Gastrointestinal Microbiome; Microbiota; DNA, Bacterial; Phylogeny; Sequence Analysis, DNA; Wolbachia; High-Throughput Nucleotide Sequencing
PubMed: 38608996
DOI: 10.1016/j.actatropica.2024.107213 -
EcoSal Plus Dec 2023Bacteriophages are viruses that infect bacteria and thus threaten industrial processes relying on the production executed by bacterial cells. Industries bear huge... (Review)
Review
Bacteriophages are viruses that infect bacteria and thus threaten industrial processes relying on the production executed by bacterial cells. Industries bear huge economic losses due to such recurring and resilient infections. Depending on the specificity of the process, there is a need for appropriate methods of bacteriophage inactivation, with an emphasis on being inexpensive and high efficiency. In this review, we summarize the reports on antiphagents, i.e., antibacteriophage agents on inactivation of bacteriophages. We focused on bacteriophages targeting the representatives of the family, as its representative, , is most commonly used in the bio-industry. The review is divided into sections dealing with bacteriophage inactivation by physical factors, chemical factors, and nanotechnology-based solutions.
Topics: Enterobacteriaceae; Bacteriophages; Escherichia coli; Viruses; Bacteria
PubMed: 36651738
DOI: 10.1128/ecosalplus.esp-0019-2022 -
The Science of the Total Environment Sep 2023Campylobacter spp. is one of the most frequent pathogens of bacterial gastroenteritis recorded worldwide. Campylobacter jejuni (C. jejuni) and Campylobacter coli (C....
Campylobacter spp. is one of the most frequent pathogens of bacterial gastroenteritis recorded worldwide. Campylobacter jejuni (C. jejuni) and Campylobacter coli (C. coli) are the two major disease-associated species, accounting for >95 % of infections, and thus have been selected for disease surveillance. Monitoring temporal variations in pathogen concentration and diversity excreted from community wastewater allows the early detection of outbreaks. Multiplex real-time/quantitative PCR (qPCR) enables multi-target quantification of pathogens in various types of samples including wastewater. Also, an internal amplification control (IAC) is required for each sample when adopting PCR-based methods for pathogen detection and quantification in wastewater to exclude the inhibition of the wastewater matrix. To achieve reliable quantification of C. jejuni and C. coli towards wastewater samples, this study developed and optimized a triplex qPCR assay by combining three qPCR primer-probe sets targeting Campylobacter jejuni subsp. jejuni, Campylobacter coli, and Campylobacter sputorum biovar sputorum (C. sputorum), respectively. This triplex qPCR assay not only can directly and simultaneously detect the concentration of C. jejuni and C. coli in wastewater but also can achieve the PCR inhibition control using C. sputorum primer-probe set. This is the first developed triplex qPCR assay with IAC for C. jejuni and C. coli, to be used in the wastewater-based epidemiology (WBE) applications. The optimized triplex qPCR assay enables the detection limit of the assay (ALOD and wastewater (PLOD) as 10 gene copy/μL and 2 log10 cells/mL (2 gene copies/μL of extracted DNA), respectively. The application of this triplex qPCR to 52 real raw wastewater samples from 13 wastewater treatment plants demonstrated its potential as a high-throughput and economically viable tool for the long-term monitoring of C. jejuni and C. coli prevalence in communities and the surrounding environments. This study provided an accessible methodology and a solid foundation for WBE-based monitoring of Campylobacter spp. relevant diseases and paved the road for future WBE back-estimation of C. jejuni and C. coli prevalence.
Topics: Campylobacter jejuni; Campylobacter coli; Wastewater; Sensitivity and Specificity; Campylobacter; DNA, Bacterial
PubMed: 37268129
DOI: 10.1016/j.scitotenv.2023.164574