Bacterial Diversity in Sediments from Lianhuan Lake, Northeast China

Lake microbiota play a crucial role in geochemical cycles, influencing both energy flow and material production. However, the distribution patterns of bacterial communities in lake sediments remain largely unclear. In this study, we used 16S rRNA high-throughput sequencing technology to investigate the bacterial structure and diversity in sediments across different locations (six independent lakes) within Lianhuan Lake and analyzed their relationship with environmental factors. Our findings revealed that both the alpha and beta diversity of sediment bacterial communities varied significantly among the six independent lakes. Furthermore, changes between lakes had a significant impact on the relative abundance of bacterial phyla, such as Pseudomonadota and Chloroflexota. The relative abundance of Pseudomonadota was highest in Habuta Lake and lowest in Xihulu Lake, while Chloroflexota abundance was lowest in Habuta Lake and highest in Tiehala Lake. At the genus level, the relative abundance of Luteitalea was highest in Xihulu Lake compared to the other five lakes, whereas the relative abundances of Clostridium, Thiobacillus, and Ilumatobacter were highest in Habuta Lake. Mantel tests and heatmaps revealed that the relative abundance of Pseudomonadota was significantly negatively correlated with pH, while the abundance of Chloroflexota was significantly positively correlated with total phosphorus and total nitrogen in water, and negatively correlated with electrical conductivity. In conclusion, this study significantly enhances our understanding of bacterial communities in the different lakes within the Lianhuan Lake watershed.

Structural and Predicted Functional Diversities of Bacterial Microbiome in Response to Sewage Sludge Amendment in Coastal Mudflat Soil

The study investigated the influence of sewage sludge application at rates of 0 (CK), 30 (ST), 75 (MT), and 150 (HT) t ha−1 to mudflats on bacterial community diversity and predicted functions using amplicon-based sequencing. Soils under sewage sludge treatments, especially the HT treatment, exhibited lower pH, salinity and higher nutrient contents (C, N, and P). Moreover, restructured bacterial communities with significantly higher diversities and distinct core and unique microbiomes were observed in all sewage sludge-amended soils as compared to the control. Specifically, core bacterial families, such as Hyphomicrobiaceae, Cytophagaceae, Pirellulaceae Microbacteriaceae, and Phyllobacteriaceae, were significantly enriched in sewage sludge-amended soils. In addition, sewage sludge amendment significantly improved predicted functional diversities of core microbiomes, with significantly higher accumulative relative abundances of functions related to carbon and nitrogen cycling processes compared to the unamended treatment. Correlation analyses showed that modified soil physicochemical properties were conducive for the improvement of diversities of bacterial communities and predicted functionalities. These outcomes demonstrated that sewage sludge amendment not only alleviated saline–sodic and nutrient deficiency conditions, but also restructured bacterial communities with higher diversities and versatile functions, which may be particularly important for the fertility formation and development of mudflat soils.

Inconsistent response of bacterial phyla diversity and abundance to soil salinity in a Chinese delta

Soil salinization is an increasingly serious problem and decreases crop yields in the Yellow River Delta (YRD), but its effects on bacterial community and diversity at the phylum level are not well known. We used high-throughput sequencing of soil bacterial 16S rRNA to identify soil bacterial communities and diversity across a gradient of soil salinity (electrical conductivity), namely, S1: low salinity level (1.78 ds/m), S2: medium salinity level (3.16 ds/m), S3: high salinity level (17.26 ds/m), S4: extreme salinity level (34.41 ds/m), and a non-salted site as the control (CK, 0.92 ds/m). Our results indicated the significantly higher values of soil C/N ratio in S2, S3, and S4 compared with that in CK. Significantly lower values of the Shannon and Chao 1 indexes were observed in S4 compared with the CK (p < 0.05). High salinity decreased the relative abundance of Actinobacteria and Acidobacteria, but increased that of Gemmatimonadetes and Bacteroidetes. Additionally, the Shannon diversity of Bacteroidetes increased by 15.5% in S4 compared with that in the CK. Our results indicate that soil salt is a main factor regulating bacterial phyla diversity and community in the extremely saline-alkaline soils of YRD. The high abundance and diversity of Bacteroidetes can be used for saline-alkali land restoration.

Bacillus amyloliquefaciens TL106 protects mice against enterohaemorrhagic Escherichia coli O157:H7-induced intestinal disease through improving immune response, intestinal barrier function and gut microbiota

AIMS

This study evaluated the effects of Bacillus amyloliquefaciens TL106, isolated from Tibetan pigs' faeces, on the growth performance, immune response, intestinal barrier function, morphology of jejunum, caecum and colon, and gut microbiota in the mice with enterohaemorrhagic Escherichia coli (EHEC)-induced intestinal diseases.

METHODS AND RESULTS

In all, 40 female C57BL/6J mice were randomly divided into four groups: mice fed a normal diet (Control), mice oral administration of TL106 daily (Ba), mice challenged with EHEC O157:H7 on day 15 (O157) and mice oral administration of TL106 daily and challenged with EHEC O157:H7 on day 15 (Ba+O157). The TL106 was administrated to mice for 14 days, and mice were infected with O157:H7 at day 15. We found that TL106 could prevent the weight loss caused by O157:H7 infection and alleviated the associated increase in pro-inflammatory factors (TNF-α, IL-1β, IL-6 and IL-8) and decrease in anti-inflammatory factor (IL-10) in serum and intestinal tissues of mice caused by O157:H7 infection (P < 0·05). Additionally, TL106 could prevent disruption of gut morphology caused by O157:H7 infection, and alleviate the associated decrease in expression of tight junction proteins (ZO-1, occludin and claudin-1) in jejunum and colon (P < 0·05). In caecum and colon, the alpha diversity for bacterial community analysis of Chao and ACE index in Ba+O157 group were higher than O157 group. The TL106 stabilized gut microbiota disturbed by O157:H7, including increasing Lachnospiraceae, Prevotellaceae, Muribaculaceae and Akkermansiaceae, and reducing Lactobacillaceae.

CONCLUSIONS

We indicated the B. amyloliquefaciens TL106 can effectively protect mice against EHEC O157:H7 infection by relieving inflammation, improving intestinal barrier function, mitigating permeability disruption and stabilizing the gut microbiota.

SIGNIFICANCE AND IMPACT OF THE STUDY

Bacillus amyloliquefaciens TL106 can prevent and treat intestinal disease induced by EHEC O157:H7 in mice, which may be a promising probiotic for disease prevention in animals.

Temporal and spatial variations in the bacterial community composition in Lake Bosten, a large, brackish lake in China

The bacteria inhabiting brackish lake environments in arid or semi-arid regions have not been thoroughly identified. In this study, the 454 pyrosequencing method was used to study the sedimentary bacterial community composition (BCC) and diversity in Lake Bosten, which is located in the arid regions of northwestern China. A total of 210,233 high-quality sequence reads and 8,427 operational taxonomic units (OTUs) were successfully obtained from 20 selected sediment samples. The samples were quantitatively dominated by members of Proteobacteria (34.1% ± 11.0%), Firmicutes (21.8% ± 21.9%) and Chloroflexi (13.8% ± 5.2%), which accounted for more than 69% of the bacterial sequences. The results showed that (i) Lake Bosten had significant spatial heterogeneity, and TOC(total organic carbon), TN(total nitrogen) and TP(total phosphorus) were the most important contributors to bacterial diversity; (ii) there was lower taxonomic richness in Lake Bosten, which is located in an arid region, than in reference lakes in eutrophic floodplains and marine systems; and (iii) there was a low percentage of dominant species in the BCC and a high percentage of unidentified bacteria. Our data help to better describe the diversity and distribution of bacterial communities in contaminated brackish lakes in arid regions and how microbes respond to environmental changes in these stable inland waters in arid or semi-arid regions.

Seasonal and spatial variation in the sediment bacterial community and diversity of Lake Bosten, China

To explore the influence of seasonal and regional environmental factors on the bacterial community composition (BCC) and diversity in the sediments of Lake Bosten, the 16S rRNA gene of sediment bacteria in four samples from the lake center area and the macrophyte-dominated area were sequenced using 454 pyrosequencing. According to the operational taxonomic units (OTUs), diversity index, relative abundance, and redundancy analysis (RDA) of the bacteria, the results showed that (i) the bacterial diversity of the lake center area was lower than that of the macrophyte-dominated area, and it was higher in winter than that in summer as a whole; (ii) seasonal factors and geographical changes had obvious effects on the abundance of dominant bacteria, including Proteobacteria and Firmicutes; (iii) a large number of unclassified bacteria were detected in this study, and the dominant unclassified genera in both lake areas included unclassified Sva0485, unclassified Anaerolineaceae, and unclassified Nitrospiraceae; and (iv) TN and TOC were the main environmental factors influencing the sediment bacterial community in Lake Bosten, as determined by RDA analysis. The study provides a reference for the in-depth understanding the impact with the change of time and space on sediment microbes in Lake Bosten.

Salinity and macrophyte drive the biogeography of the sedimentary bacterial communities in a brackish water tropical coastal lagoon

Brackish water coastal lagoons are least understood with respect to the seasonal and temporal variability in their sedimentary bacterial communities. These coastal lagoons are characterized by the steep environmental gradient and provide an excellent model system to decipher the biotic and abiotic factors that determine the bacterial community structure over time and space. Using Illumina sequencing of the 16S rRNA genes from a total of 100 bulk surface sediments, we investigated the sedimentary bacterial communities, their spatiotemporal distribution, and compared them with the rhizosphere sediment communities of a common reed; Phragmites karka and a native seagrass species; Halodule uninervis in Chilika Lagoon. Spatiotemporal patterns in bacterial communities were linked to specific biotic factors (e.g., presence and type of macrophyte) and abiotic factors (e.g., salinity) that drove the community composition. Comparative assessment of communities highlighted bacterial lineages that were responsible for segregating the sediment communities over distinct salinity regimes, seasons, locations, and presence and type of macrophytes. Several bacterial taxa were specific to one of these ecological factors suggesting that species-sorting processes drive specific biogeographical patterns in the bacterial populations. Modeling of proteobacterial lineages against salinity gradient revealed that α- and γ-Proteobacteria increased with salinity, whereas β-Proteobacteria displayed the opposite trend. The wide variety of biogeochemical functions performed by the rhizosphere microbiota of P. karka must be taken into consideration while formulating the management and conservation plan for this reed. Overall, this study provides a comprehensive understanding of the spatiotemporal dynamics and functionality of sedimentary bacterial communities and highlighted the role of biotic and abiotic factors in generating the biogeographical patterns in the bacterial communities of a tropical brackish water coastal lagoon.