Responses of Acidobacteria Granulicella sp. WH15 to High Carbon Revealed by Integrated Omics Analyses

Metagenomics and network analysis decipher profiles and co-occurrence patterns of bacterial taxa in soils amended with biogas slurry

Microbial community and interaction play crucial roles in ecological functions of soil including nutrient cycling carbon storage, and water maintenance etc. Numerous studies have shown that the application of fertilizers alters bacterial diversity; However, it remains unknown whether and how the continuous application of biogas slurry from anaerobic digestion affects the spatiotemporal heterogeneity of soil layers, complexity and stability of microbial networks, and functions related to C and N cycling. Here, we investigated the bacterial taxa of purple soils treated with swine biogas slurry for four different periods (0, 1, 3 and 8 years) and five different soil depths (20, 40, 60, 80 and 100 cm). The results showed that the application period of biogas slurry and soil depth were two powerful drivers of bacterial diversity and communities. Biogas slurry input resulted in marked changes in the bacterial diversity and composition at the soil depths of 0-60 cm. The relative abundances of Acidobacteriota, Myxococcot, and Nitrospirota decreased, while Actinobacteria, Chloroflexi, and Gemmatimonadota increased with repeated biogas slurry input. The decreasing complexity and stability of the bacterial network with decreasing nodes, links, robustness, and cohesions were found with increasing years of biogas slurry application, suggesting that the bacterial network of soils treated by the biogas slurry became more vulnerability compared with the control. Also, the linkages between the keystone taxa and soil properties were weakened after biogas slurry input, leading to the cooccurrence patterns being less affected by the keystones in the high level of nutrients. Metagenomic analysis confirmed that biogas slurry input increased the relative abundance of liable-C degradation and denitrification genes, which could highly impact the network properties. Overall, our study could give comprehensive understandings on the impacts of biogas slurry amendment on soils, which could be useful for maintaining sustainable agriculture and soil health with liquid fertilization.

Bacteriome composition analysis of selected mineral water occurrences in Serbia

Bacterial metabarcoding analysis by 16S rDNA of five occurrences of mineral waters in Serbia (Torda, Slankamen Banja, Lomnicki Kiseljak, Velika Vrbnica and Obrenovacka Banja) indicated the presence of a high percentage of the Proteobacteria phylum, followed by the Bacteroidetes phylum. The families Rhodobacteraceae, Burkholderiaceae, Pseudomonadaceae, Methylophilaceae and Moraxellaceae were the most dominant in the bacterial flora of the selected occurrences, whereas the most represented genera were Acinetobacter, Pseudorhodobacter, Pseudomonas, Limnohabitans, Massilia, Limnobacter and Methylotenera. The presence of coliform bacteria was not detected. Alpha diversity analysis revealed that Slankamen Banja and Lomnicki Kiseljak were the richest of the selected occurrences, while the mineral waters of Torda, Velika Vrbnica and Obrenovacka Banja were characterized by similar diversity of bacterial communities determined by beta diversity analysis. Physical-chemical analysis revealed the value of total dissolved solids above 1 g/L, as well as elevated concentrations of some metals and non-metals. The research concluded that specific bacteria contribute to the development of biocorrosion and biofouling processes of water intake facilities. In addition, some of these bacteria might be potential indicators of the organic sources of pollution and/or biotechnological natural remediators in the treatment of contaminated waters.

Impact of Different Trace Elements on the Growth and Proteome of Two Strains of Granulicella, Class "Acidobacteriia"

Acidobacteria represents one of the most dominant bacterial groups across diverse ecosystems. However, insight into their ecology and physiology has been hampered by difficulties in cultivating members of this phylum. Previous cultivation efforts have suggested an important role of trace elements for the proliferation of Acidobacteria, however, the impact of these metals on their growth and metabolism is not known. In order to gain insight into this relationship, we evaluated the effect of trace element solution SL10 on the growth of two strains (5B5 and WH15) of Acidobacteria belonging to the genus Granulicella and studied the proteomic responses to manganese (Mn). Granulicella species had highest growth with the addition of Mn, as well as higher tolerance to this metal compared to seven other metal salts. Variations in tolerance to metal salt concentrations suggests that Granulicella sp. strains possess different mechanisms to deal with metal ion homeostasis and stress. Furthermore, Granulicella sp. 5B5 might be more adapted to survive in an environment with higher concentration of several metal ions when compared to Granulicella sp. WH15. The proteomic profiles of both strains indicated that Mn was more important in enhancing enzymatic activity than to protein expression regulation. In the genomic analyses, we did not find the most common transcriptional regulation of Mn homeostasis, but we found candidate transporters that could be potentially involved in Mn homeostasis for Granulicella species. The presence of such transporters might be involved in tolerance to higher Mn concentrations, improving the adaptability of bacteria to metal enriched environments, such as the decaying wood-rich Mn environment from which these two Granulicella strains were isolated.