Background: Natural environments nurture numerous and diverse microorganisms, playing essential roles in material cycle, energy flow, environmental protection and human health. However, because microorganisms represent “the unseen majority”, the lack of pure cultures makes it challenging to explore the biochemical and physiological features of microorganisms. The high complexity of microbial community also makes it difficult to conduct in-situ identification and characterization of microbial metabolism. Nowadays, these limitations could be alleviated by molecular biological techniques and high-throughput sequencing approaches. With the rapid development of molecular techniques such as microanalysis and biomarkers, many novel lineages have been discovered and isolated, and new microbial metabolic pathways have been elucidated, continuously expanding our understanding of environmental microorganisms. However, there are still many unknown metabolic pathways and functions that may play important roles in global changes and remain to be explored. Thus, the ongoing efforts to uncover novel species and mechanisms of their evolutionary potential and environmental adaption are of great significance. Our research is committed to exploring the microbial resources for key biogeochemical cycles and organic pollutant degradation and characterizing their ecological functions, with the aim to advance applications in the fields of water eutrophication, greenhouse gas emission reduction, and bioremediation of polluted environments.
Progress: Great efforts have been made to explore resources of environmental microorganisms related to the control of harmful algae, degradation of petroleum hydrocarbon and conversion of nitrogen pollutants. Up to now, over 500 strains have been obtained across estuary, offshore, mangrove and marine regions, and 23 novel genus/species have been published. They hold promising applications in the field of environmental purification, such as Chitinimonas prasina with capability of killing harmful algae directly, mixotrophic bacterium Nitrogeniibacter mangrovi with flexible metabolic potential and lots of strains with the ability of petroleum and polycyclic aromatic hydrocarbons (PAHs) degradation. The biodegradation of high-molecular-weight PAHs (HMW-PAHs) remains a great challenge. Based on pure cultures of PAHs degraders, further studies were conducted using molecular techniques to reveal metabolic networks of PAHs biodegradation and identify the genetic resources for PAHs catabolism, contributing to the improvement of HMW-PAHs biodegradation. Regarding the HMW-PAH Benzo[a]pyrene (BaP) as a targeted contaminant and Novosphingobium pentaromativorans US6-1 as a model degrading strain, multiple approaches such as comparative transcriptomics, knock-out experiments, metabolomics were used in our studies to reveal the molecular mechanisms of US6-1 underlying the sense, transport and degradation of HMW-PAHs, aiming at targeted enhancement of specific microbial functions and providing valuable clues for the improvement of HMW-PAHs biodegradation efficiency. Studies on HMW-PAHs biodegradation at microbiome level were also launched, using mangrove-sediments-based microcosms under BaP contamination as the research objects. Using 16S rRNA gene sequencing and metagenomics approaches, we revealed the microbial diversity, community succession, turnover of polymicrobial interactions and keystone taxa under BaP contamination along with their functional responses to BaP contamination, highlighting the importance of helper bacteria for BaP degradation and providing clues for the construction of efficiently degrading consortium. In addition, the application of cultivation and meta-omics methods facilitated to discover the novel and mangrove specific lineages that drive key biogeochemical processes such as anammox and denitrification-dependent anaerobic methane oxidation, emending the model of global nitrogen cycle.
Perspective: In light of molecular biology, meta-omics and bioinformatics, our understanding of microorganisms has been expended from “producer” and “degrader” to the “driver” and “linker” of key biochemical cycles and the “indicator” and “regulator” of environmental changes. Microorganisms may play other unknown roles that await to be explored. Based on pure culture research, it is expected to discover and clarify novel pathways and mechanisms of microbial metabolism at molecular and cellular levels, providing molecular elements and engineering strategies for the optimization of microbial functions. The environmental microorganism research is essential for the realization of intelligent degradation of environmental pollutants in model organisms and green synthesis of target compounds, and provides biomarkers and strategies to trace, identify and promote microbial functioning for ecosystems and engineering systems. In-depth research on metabolic mechanisms at the microbiome level allows us to discover new processes in the element cycles, reveal the coupling mechanisms among different processes, understand the microbe-to-microbe and microbe-to-environment interactions across spatio-temporal scales, and to realize the microbial characterization of biogeochemical cycles and prediction of ecosystem functions in the context of global changes. These studies can provide theoretical and technical support for addressing major issues related to economic and social development.