Jinyuan Li, Han Li, Zhuo Pan, Di Sun, Jiahao Wang, Wenkun Zhang, Gang Pan. Findings of the Association for Computational Linguistics: EMNLP 2023. 2023.

Summary: Estuaries connect rivers with the ocean and are considered transition regions due to the continuous inputs from rivers. Microbiota from different sources converge and undergo succession in these transition regions, but their assembly mechanisms along environmental gradients remain unclear. Here, we found that salinity had a stronger effect on planktonic than on benthic microbial communities, and the dominant planktonic bacteria changed more distinctly than the dominant benthic bacteria with changes in salinity. The planktonic bacteria in the brackish water came mainly from seawater, which was confirmed in the laboratory, whereas the benthic bacteria were weakly affected by salinity, which appeared to be a mixture of the bacteria from riverine and oceanic sediments. Benthic bacterial community assembly in the sediments was mainly controlled by homogeneous selection and almost unaffected by changes in salinity, the dominant assemblage processes for planktonic bacteria changed dramatically along the salinity gradient, from homogeneous selection in freshwater to drift in seawater. Our results highlight that salinity is the key driver of estuarine microbial succession and that salinity is more important in shaping planktonic than benthic bacterial communities in the Yellow River estuary.

Climate change is profoundly affecting human health. Human pathogenic bacteria (HPB) infections mediated by the environment are considered a substantial cause of global health losses. However, the biogeography of HPB and their response to climate change remain largely unknown. Here, we constructed and analyzed a global atlas of potential HPB using 1,066,584 samples worldwide. HPB are widely present in the global environment, and their distribution follows a latitudinal diversity gradient. Climate and anthropogenic factors are identified as major drivers of the global distribution of HPB. Our predictions indicated that by the end of this century, the richness, abundance, and invasion risk of HPB will increase globally, with this upward trend becoming more pronounced as development sustainability declines. Therefore, the threat of environmentally mediated HPB infections to human health may be more severe in a world where anthropogenic activities are intensifying and the global climate is warming.

The chaperone 70 kDa heat shock protein (Hsp70) is important for cells from bacteria to humans to maintain proteostasis, and all eukaryotes and several prokaryotes encode Hsp70 paralogs. Although the mechanisms of Hsp70 function have been clearly illuminated, the function and evolution of Hsp70 paralogs is not well studied. DnaK is a highly conserved bacterial Hsp70 family. Here, we show that dnaK is present in 98.9% of bacterial genomes, and 6.4% of them possess two or more DnaK paralogs. We found that the duplication of dnaK is positively correlated with an increase in proteomic complexity (proteome size, number of domains). We identified the interactomes of the two DnaK paralogs of Myxococcus xanthus DK1622 (MxDnaKs), which revealed that they are mostly nonoverlapping, although both prefer α and β domain proteins. Consistent with the entire M. xanthus proteome, MxDnaK substrates have both significantly more multi-domain proteins and a higher isoelectric point than that of Escherichia coli , which encodes a single DnaK homolog. MxDnaK1 is transcriptionally upregulated in response to heat shock and prefers to bind cytosolic proteins, while MxDnaK2 is downregulated by heat shock and is more associated with membrane proteins. Using domain swapping, we show that the nucleotide-binding domain and the substrate-binding β domain are responsible for the significant differences in DnaK interactomes, and the nucleotide binding domain also determines the dimerization of MxDnaK2, but not MxDnaK1. Our work suggests that bacterial DnaK has been duplicated in order to deal with a more complex proteome, and that this allows evolution of distinct domains to deal with different subsets of target proteins. IMPORTANCE: All eukaryotic and ~40% of prokaryotic species encode multiple 70 kDa heat shock protein (Hsp70) homologs with similar but diversified functions. Here, we show that duplication of canonical Hsp70 (DnaK in prokaryotes) correlates with increasing proteomic complexity and evolution of particular regions of the protein. Using the Myxococcus xanthus DnaK duplicates as a case, we found that their substrate spectrums are mostly nonoverlapping, and are both consistent to that of Escherichia coli DnaK in structural and molecular characteristics, but show differential enrichment of membrane proteins. Domain/region swapping demonstrated that the nucleotide-binding domain and the β substrate-binding domain (SBDβ), but not the SBDα or disordered C-terminal tail region, are responsible for this functional divergence. This work provides the first direct evidence for regional evolution of DnaK paralogs.

Hsp70 proteins are highly conserved chaperones that occur in all kingdoms of life. Multiple copies of Hsp70s are often present in genome-sequenced prokaryotes, especially taxa with complex life cycles, such as myxobacteria.

Climate change impacts microbial community structure and function, thus altering biogeochemical cycles. Biological nitrogen fixation by diazotrophs is involved in maintaining the balance of the global nitrogen cycle, but the global biogeographic patterns of diazotrophs and their responses to climate change remain unclear. In this study, we use a dataset of 1352 potential diazotrophs by leveraging the co-occurrence of nitrogenase genes (nifHDK) and analyse the global distribution of potential diazotrophs derived from 137,672 samples. Using the random forest model, we construct a global map of diazotroph diversity, revealing spatial variations in diversity across large scales. Feature importance shows that precipitation and temperature may act as drivers of diazotroph diversity, as these factors explain 54.2% of the variation in the global distribution of diazotroph diversity. Using projections of future climate under different shared socioeconomic pathways, we show that overall diazotroph diversity could decline by 1.5%-3.3%, with this decline further exacerbated by development patterns that increase carbon emissions. Our findings highlight the importance of sustainable development in preserving diazotrophs.