Strong linkage between nutrient-cycling functional gene diversity and ecosystem multifunctionality during winter composting with pig manure and fallen leaves.

Microorganisms play important roles in element transformation and display distinct compositional changes during composting. However, little is known about the linkage between nutrient-cycling functional gene diversity and compost ecosystem multifunctionality (EMF). This study performed winter composting with pig manure and fallen leaves and evaluated the distribution patterns and ecological roles of multiple functional genes involved in nutrient cycles. Physicochemical properties and enzyme activities presented large fluctuations during composting. Absolute abundance, composition, and diversity of functional genes participating in carbon, nitrogen, phosphorus, and sulfur cycles presented distinct dynamic changes. Stronger linkage was found between enzyme activities and temperature than other physicochemical factors, whereas total nitrogen rather than other physicochemical factors displayed closer linkage with functional gene composition and diversity. EMF targeting key nutrient (i.e., carbon, nitrogen, phosphorus, and sulfur) cycles was significantly positively correlated with temperature and notably negatively correlated with functional gene diversity. Enzyme activities rather than functional gene diversity showed a greater potential effect on phosphorus availability. Consequently, the available phosphorus (AP) content increased from initial 0.50 g/kg to final 1.43 g/kg. To our knowledge, this is the first study that deciphered ecological roles of nutrient-cycling functional gene diversity during composting, and the final compost can serve as a potential phosphorus fertilizer.

Abundance and diversity of eukaryotic rather than bacterial community relate closely to the trophic level of urban lakes.

Scientific understanding of biotic effects on the water trophic level is lacking for urban lakes during algal bloom development stage. Based on the Illumina MiSeq sequencing, quantitative polymerase chain reaction (PCR), and multiple statistical analyses, we estimated distribution patterns and ecological roles of planktonic bacteria and eukaryotes in urban lakes during algal bloom development stage (i.e., April, May, and June). Cyanobacteria and Chlorophyta mainly dominated algal blooms. Bacteria exhibited significantly higher absolute abundance and community diversity than eukaryotes, whereas abundance and diversity of eukaryotic rather than bacterial community relate closely to the water trophic level. Multinutrient cycling (MNC) index was significantly correlated with eukaryotic diversity rather than bacterial diversity. Stronger species replacement, broader environmental breadth, and stronger phylogenetic signal were found for eukaryotic community than for bacterial community. In contrast, bacterial community displayed stronger community stability and environmental constraint than eukaryotic community. Stochastic and differentiating processes contributed more to community assemblies of bacteria and eukaryotes. Our results emphasized that a strong linkage between planktonic diversity and MNC ensured a close relationship between planktonic diversity and the water trophic level of urban lakes. Our findings could be useful to guide the formulation and implementation of environmental lake protection measures.

New insights into the function of the proteins IsiC and IsiD from Synechocystis sp. PCC 6803 under iron limitation.

Iron is a common cofactor in biological processes such as respiration, photosynthesis, and nitrogen fixation. The genes isiC and isiD encode unknown proteins, and the growth of ΔisiC and ΔisiD mutants is inhibited under iron-deficient conditions. To study the regulatory mechanisms of IsiC and IsiD during iron starvation, we carried out transcriptome and metabolome sequencing. The Kyoto Encyclopedia of Genes and Genomes (KEGG) analysis showed that the photosynthesis, nitrogen metabolism, and ABC transporter pathways play a vital role in regulating iron deficiency. Upon iron repletion, IsiC and IsiD also have a regulatory effect on these pathways. Additionally, KEGG analysis of the differential metabolites of wild type (WT) and mutants showed that they were all enriched in starch and sucrose metabolism after iron limitation. Weighted gene co-expression network analysis (WGCNA) constructed a co-expression network of differentially expressed genes with phenotypes and metabolites, and finally identified five modules. The turquoise module was positively correlated with iron deficiency. In contrast, the WT and blue module exhibited a negative correlation, and the mutants ΔisiC and ΔisiD were positively correlated with the gray and brown modules, respectively. WGCNA also analyzed the relationship between metabolites and phenotypes, and the green module was related to iron starvation. The co-expression network determined the hub genes and metabolites of each module. This study lays a foundation for a better understanding of cyanobacteria in response to iron deficiency. KEY POINTS: • Nitrogen metabolism and ABC transporters are involved in iron regulation. • Starch and sucrose metabolism is related to the regulation of iron deficiency. • WGCNA analyzes the correlation between genes and metabolites.

Function analysis of RNase E in the filamentous cyanobacterium Anabaena sp. PCC 7120.

RNase E is an endoribonuclease and plays a central role in RNA metabolism. Cyanobacteria, as ancient oxygen-producing photosynthetic bacteria, also contain RNase E homologues. Here, we introduced mutations into the S1 subdomain (F53A), the 5'-sensor subdomain (R160A), and the DNase I subdomain (D296A) according to the key activity sites of Escherichia coli RNase E. The results of degradation assays demonstrated that Asp296 is important to RNase E activity in Anabaena sp. PCC 7120 (hereafter PCC 7120). The docking model of RNase E in PCC 7120 (AnaRne) and RNA suggested a possible recognition mechanism of AnaRne to RNA. Moreover, overexpression of AnaRne and its N-terminal catalytic domain (AnaRneN) in vivo led to the abnormal cell division and inhibited the growth of PCC 7120. The quantitative analysis showed a significant decrease of ftsZ transcription in the case of overexpression of AnaRne or AnaRneN and ftsZ mRNA could be directly degraded by AnaRne through degradation assays in vitro, indicating that AnaRne was related to the expression of ftsZ and eventually affected cell division. In essence, our studies expand the understanding of the structural and functional evolutionary basis of RNase E and lay a foundation for further analysis of RNA metabolism in cyanobacteria.

Transcriptome Analysis Reveals IsiA-Regulatory Mechanisms Underlying Iron Depletion and Oxidative-Stress Acclimation in Synechocystis sp. Strain PCC 6803.

Microorganisms in nature are commonly exposed to various stresses in parallel. The isiA gene encodes an iron stress-induced chlorophyll-binding protein which is significantly induced under iron starvation and oxidative stress. Acclimation of oxidative stress and iron deficiency was investigated using a regulatory mutant of the Synechocystis sp. strain PCC 6803. In this study, the ΔisiA mutant grew more slowly in oxidative-stress and iron depletion conditions compared to the wild-type (WT) counterpart under the same conditions. Thus, we performed transcriptome sequencing (RNA-seq) analysis of the WT strain and the ΔisiA mutant under double-stress conditions to obtain a comprehensive view of isiA-regulated genes. Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) enrichment analyses showed significant differences between the WT strain and ΔisiA mutant, mainly related to photosynthesis and the iron-sulfur cluster. The deletion of isiA affects the expression of various genes that are involved in cellular processes and structures, such as photosynthesis, phycobilisome, and the proton-transporting ATPase complex. Weighted gene coexpression network analysis (WGCNA) demonstrated three functional modules in which the turquoise module was negatively correlated with superoxide dismutase (SOD) activity. Coexpression network analysis identified several hub genes of each module. Cotranscriptional PCR and reads coverage using the Integrative Genomics Viewer demonstrated that isiA, isiB, isiC, ssl0461, and dfp belonged to the isi operon. Three sRNAs related to oxidative stress were identified. This study enriches our knowledge of IsiA-regulatory mechanisms under iron deficiency and oxidative stress.IMPORTANCE This study analyzed the impact of isiA deletion on the transcriptomic profile of Synechocystis The isiA gene encodes an iron stress-induced chlorophyll-binding protein, which is significantly induced under iron starvation. The deletion of isiA affects the expression of various genes that are involved in photosynthesis and ABC transporters. WGCNA revealed three functional modules in which the blue module was correlated with oxidative stress. We further demonstrated that the isi operon contained the following five genes: isiA, isiB, isiC, ssl0461, and dfp by cotranscriptional PCR. Three sRNAs were identified that were related to oxidative stress. This study enhances our knowledge of IsiA-regulatory mechanisms under iron deficiency and oxidative stress.