The relationships of present vegetation, bacteria, and soil properties with soil organic matter characteristics in moist acidic tundra in Alaska

Acidobacteria members harbour an abundant and diverse carbohydrate-active enzymes (cazyme) and secreted proteasome repertoire, key factors for potential efficient biomass degradation

The Acidobacteria phylum is a very abundant group (20-30% of microbial communities in soil ecosystems); however, little is known about these microorganisms and their ability to degrade the biomass and lignocellulose due to the difficulty of culturing them. We, therefore, bioinformatically studied the content of lignocellulolytic enzymes (total and predicted secreted enzymes) and secreted peptidases in an in silico library containing 41 Acidobacteria genomes. The results showed a high abundance and diversity of total and secreted Carbohydrate-Active enzymes (cazyme) families among the Acidobacteria compared to known previous degraders. Indeed, the relative abundance of cazymes in some genomes represented more than 6% of the gene coding proteins with at least 300 cazymes. The same observation was made with the predicted secreted peptidases with several families of secreted peptidases, which represented at least 1.5% of the gene coding proteins in several genomes. These results allowed us to highlight the lignocellulolytic potential of the Acidobacteria phylum in the degradation of lignocellulosic biomass, which could explain its high abundance in the environment.

Application of microalgae Scenedesmus acuminatus enhances water quality in rice-crayfish culture

Improper management of aquatic environments substantially restricts the development of the aquaculture industry. The industrialisation of the crayfish Procambarus clarkii, for example, is currently being limited by poor water quality. Research suggests that microalgal biotechnology has a great potential for water quality regulation. However, the ecological effects of microalgal applications on aquatic communities in aquaculture systems remain largely unknown. In the present study, 5 L Scenedesmus acuminatus GT-2 culture (biomass 120 g L^-1) was added to an approximately 1,000 m² rice-crayfish culture to examine the response of aquatic ecosystems to microalgal application. The total nitrogen content decreased significantly as a result of microalgal addition. Moreover, the microalgal addition changed the bacterial community structure directionally and produced more nitrate reducing and aerobic bacteria. The effect of microalgal addition on plankton community structure was not obvious, except for a significant difference in Spirogyra growth which was inhibited by 81.0% under microalgal addition. Furthermore, the network of microorganisms in culture systems with the added microalga had higher interconnectivity and was more complex, which indicating microalgal application enhance the stability of aquaculture systems. The application of microalgae was found to have the greatest effect on the 6th day of the experiment, as supported by both environmental and biological evidence. These findings can provide valuable guidance for the practical application of microalgae in aquaculture systems.

Linkages between the molecular composition of dissolved organic matter and soil microbial community in a boreal forest during freeze-thaw cycles

Soil dissolved organic matter (DOM) plays a vital role in biogeochemical processes. Global warming leads to increased freeze-thaw cycles (FTCs) in boreal forest soils, which can change DOM production and consumption. However, the interactions between the chemical composition of DOM molecules and the microbial communities that drive C decomposition in the context of freeze-thaw are poorly understood. Here, a FTCs incubation experiment was conducted. Combined with pyrolysis gas chromatography-mass spectrometry and high-throughput sequencing techniques, the relationships between DOM chemodiversity and microbial community structure were assessed. Results indicated that both low-frequency (2FTCs) and high-frequency freeze-thaw cycles (6FTCs) significantly increased soil dissolved organic carbon (DOC) contents in the surface (0-10 cm) and subsurface (50-60 cm) soil layers. In the topsoil, FTCs significantly reduced the relative abundance of aromatic compounds, but increased the relative proportions of alkanes, phenols, fatty acid methyl esters (Me) and polysaccharides in the DOM. In the subsuface soil layer, only the relative abundance of Me in the 6FTCs treatment increased significantly. The response of bacterial communities to FTCs was more sensitive than that of fungi, among which only the relative abundance of Gammaproteobacteria increased by FTCs. Moreover, the relative abundance of these taxa was positively correlated with the increment of DOC. Co-occurrence networks confirmed DOM-bacterial interactions, implying that specific microorganisms degrade specific substrates. At class level, Gammaproteobacteria were significantly positively correlated with labile C (polysaccharides and alkanes), whereas other bacterial classes such as Actinobacteria, Alphaproteobacteria, and Thermoleophilia were significantly positively correlated with aromatic compounds in the topsoil. Collectively, FTCs tended to activate DOM and enhance its biodegradability of DOM, potentially hampering DOC accumulation and C sequestration. These findings highlight the potential of DOM molecular mechanisms to regulate the functional states of soil bacterial communities under increased FTCs.

Petroleum pollution affects soil chemistry and reshapes the diversity and networks of microbial communities

Soil is the bearing centre of terrestrial ecosystems. Oil pollution leads to changes in the physical and chemical properties of soil to varying degrees. Polluted soils form a unique microbial species composition, which provides rich materials for the bioremediation of oil-contaminated soil through biological enhancement. Understanding the microbial composition of petroleum-contaminated soil can provide a better biological method for soil remediation. Based on this, 16 S rRNA and ITS genetic markers were used to analyse the bacterial and fungal microbiota in petroleum-contaminated soil, and their physical and chemical properties (total organic carbon, alkaline hydrolysable nitrogen, total phosphorus, total potassium, available potassium, Cu, Zn, and Cd) were measured. It was found that petroleum pollution can significantly reduce the abundance and diversity of bacteria and fungi in the soil and significantly promote the relative abundance of Proteobacteria, Pseudomonas, Pseudoxanthomonas and Pseudoallescheria, which changed the dominant flora of bacteria and fungi and reshaped the co-occurrence network relationship between bacteria and fungi in oil-contaminated soil. The content of total organic carbon in petroleum-contaminated soil was significantly higher than that in uncontaminated soil, while the content of alkaline hydrolysable nitrogen and available potassium was significantly lower than that in uncontaminated soil, and the content of Cu significantly increased after pollution. Total organic carbon is the key driving factor that changes oil-contaminated soil microorganisms and plays a significant role in regulating the remodelling and composition of the microbial community in oil-contaminated soil. This study laid a solid theoretical foundation for the bioremediation of oil-contaminated soil.

Evaluation of phoxim toxicity on aquatic and zebrafish intestinal microbiota by metagenomics and 16S rRNA gene sequencing analysis

Phoxim is one of the main organophosphorus pesticides used in agricultural production. However, little information is known about how it affects the aquatic microbial community and the intestinal microbiota of fish. Herein, we utilized shotgun metagenomics and 16S rRNA gene sequencing to reveal the aquatic eco-risk of phoxim. Seven days of phoxim exposure significantly changed the composition of aquatic microbial community, obliterated the interactions between microorganisms, and thus reduced the complexity and stability of the microbial community. During long-time exposure (i.e., 14 days), most of the ecological functions were restored due to the redundancy of the microbial community. However, phoxim exposure promoted the dissemination of elfamycin resistance gene. The zebrafish gut microbial community also recovered from a temporary ecological disorder of aquatic microbiota, but phoxim continually affected zebrafish growth and swimming behavior. Overall, our results demonstrated that phoxim exposure significantly changed the structure and function of the microbial community and displayed a negative impact on freshwater ecosystems in a short exposure time.