Unique microbiome in organic matter–polluted urban rivers

Approximately half of the global annual production of wastewater is released untreated into aquatic environments, which results in worldwide organic matter pollution in urban rivers, especially in highly populated developing countries. Nonetheless, information on microbial community assembly and assembly-driving processes in organic matter–polluted urban rivers remains elusive. In this study, a field study based on water and sediment samples collected from 200 organic matter–polluted urban rivers of 82 cities in China and Indonesia is combined with laboratory water-sediment column experiments. Our findings demonstrate a unique microbiome in these urban rivers. Among the community assembly-regulating factors, both organic matter and geographic conditions play major roles in determining prokaryotic and eukaryotic community assemblies, especially regarding the critical role of organic matter in regulating taxonomic composition. Using a dissimilarity-overlap approach, we found universality in the dynamics of water and sediment community assembly in organic matter–polluted urban rivers, which is distinctively different from patterns in eutrophic and oligotrophic waters. The prokaryotic and eukaryotic communities are dominated by deterministic and stochastic processes, respectively. Interestingly, water prokaryotic communities showed a three-phase cyclic succession of the community assembly process before, during, and after organic matter pollution. Our study provides the first large-scale and comprehensive insight into the prokaryotic and eukaryotic community assembly in organic matter–polluted urban rivers and supports their future sustainable management.     

The microbe-mediated mechanisms affecting topsoil carbon stock in Tibetan grasslands

Warming has been shown to cause soil carbon (C) loss in northern grasslands owing to accelerated microbial decomposition that offsets increased grass productivity. Yet, a multi-decadal survey indicated that the surface soil C stock in Tibetan alpine grasslands remained relatively stable. To investigate this inconsistency, we analyzed the feedback responses of soil microbial communities to simulated warming by soil transplant in Tibetan grasslands. Whereas microbial functional diversity decreased in response to warming, microbial community structure did not correlate with changes in temperature. The relative abundance of catabolic genes associated with nitrogen (N) and C cycling decreased with warming, most notably in genes encoding enzymes associated with more recalcitrant C substrates. By contrast, genes associated with C fixation increased in relative abundance. The relative abundance of genes associated with urease, glutamate dehydrogenase and ammonia monoxygenase (ureC, gdh and amoA) were significantly correlated with N₂O efflux. These results suggest that unlike arid/semiarid grasslands, Tibetan grasslands maintain negative feedback mechanisms that preserve terrestrial C and N pools. To examine whether these trends were applicable to the whole plateau, we included these measurements in a model and verified that topsoil C stocks remained relatively stable. Thus, by establishing linkages between microbial metabolic potential and soil biogeochemical processes, we conclude that long-term C loss in Tibetan grasslands is ameliorated by a reduction in microbial decomposition of recalcitrant C substrates.     

Interdomain ecological networks between plants and microbes

While macroscopic interkingdom relationships have been intensively investigated in various ecosystems, the above–belowground ecology in natural ecosystems has been poorly understood, especially for the plant–microbe associations at a regional scale. In this study, we proposed a workflow to construct interdomain ecological networks (IDEN) between multiple plants and various microbes (bacteria and archaea in this study). Across 30 latitudinal forests in China, the regional IDEN showed particular topological features, including high connectance, nested structure, asymmetric specialization and modularity. Also, plant species exhibited strong preference to specific microbial groups, and the observed network was significantly different from randomly rewired networks. Network module analysis indicated that a majority of microbes associated with plants within modules rather than across modules, suggesting specialized associations between plants and microorganisms. Consistent plant–microbe associations were captured via IDENs constructed within individual forest locations, which reinforced the validity of IDEN analysis. In addition, the plant–forest link distribution showed the geographical distribution of plants had higher endemicity than that of microorganisms. With cautious experimental design and data processing, this study shows interdomain species associations between plants and microbes in natural forest ecosystems and provides new insights into our understanding of meta‐communities across different domain species.     

The role of S-nitrosylation of PFKM in regulation of glycolysis in ovarian cancer cells

One of the malignant transformation hallmarks is metabolism reprogramming, which plays a critical role in the biosynthetic needs of unchecked proliferation, abrogating cell death programs, and immunologic escape. However, the mechanism of the metabolic switch is not fully understood. Here, we found that the S-nitrosoproteomic profile of endogenous nitrogen oxide in ovarian cancer cells targeted multiple components in metabolism processes. Phosphofructokinase (PFKM), one of the most important regulatory enzymes of glycolysis, was S-nitrosylated by nitric oxide synthase NOS1 at Cys351. S-nitrosylation at Cys351 stabilized the tetramer of PFKM, leading to resist negative feedback of downstream metabolic intermediates. The PFKM-C351S mutation decreased the proliferation rate of cultured cancer cells, and reduced tumor growth and metastasis in the mouse xenograft model. These findings indicated that S-nitrosylation at Cys351 of PFKM by NOS1 contributes to the metabolic reprogramming of ovarian cancer cells, highlighting a critical role of endogenous nitrogen oxide on metabolism regulations in tumor progression.Subject terms: Cancer metabolism, Nitrosylation     

Complete Genome Sequence of Two Variant Porcine Reproductive and Respiratory Syndrome Viruses Isolated from Vaccinated Piglets

Porcine reproductive and respiratory syndrome virus (PRRSV) continues to affect the Chinese swine industry. Since 2006, variant PRRSV strains sharing two unique discontinuous deletions of 30 amino acids in the nonstructural protein Nsp2 have become dominant in Chinese swine herds and have caused huge economic losses to the swine industry in China. Here we report the complete genome sequence of two novel PRRSV variants isolated from vaccinated piglets with additional amino acid deletions in Nsp2.     

Wnt/β-catenin signaling mediates the abnormal osteogenic and adipogenic capabilities of bone marrow mesenchymal stem cells from chronic graft-versus-host disease patients

Chronic graft-versus-host disease (cGVHD) is the main cause of non-relapse mortality after allogeneic hematopoietic stem cell transplantation (allo-HSCT). Mesenchymal stem cells (MSCs) in bone marrow (BM) remain unclear in the pathophysiology of cGVHD. In this study, we analyzed BM-MSCs from 66 patients after allo-HSCT, including 33 with active cGVHD and 33 without cGVHD. BM-MSCs showed similar morphology, frequency, phenotype, and proliferation in patients with or without cGVHD. MSCs from the active cGVHD group showed a decreased apoptosis rate (P < 0.01). Osteogenic capacity was increased while adipogenic capacity was decreased in the active cGVHD MSCs compared with no-cGVHD MSCs. The expressions of osteogenic gene RUNX2 and COL1A1 were higher (P < 0.001) while adipogenic gene PPAR-γ and FABP4 were lower (P < 0.001) in the active cGVHD MSCs than no-cGVHD MSCs. These changes were associated with the severity of cGVHD (P < 0.0001; r = 0.534, r = 0.476, r = −0.796, and r = −0.747, respectively in RUNX2, COL1A1, PPAR-γ, and FABP4). The expression of Wnt/β-catenin pathway ligand Wnt3a was increased in cGVHD-MSCs. The dysfunction of cGVHD-MSCs could be reversed by Dickkopf related protein 1(DKK1) to inhibit the binding of Wnt3a. In summary, the differentiation of BM-MSCs was abnormal in active cGVHD, and its underlying mechanism is the upregulated of Wnt3a through Wnt/β-catenin signaling pathway of MSCs.Subject terms: Cell signalling, Mesenchymal stem cells