Understanding adaptation of biological communities to environmental change is a central issue in ecology and evolution. Metagenomic analysis of a stressed groundwater microbial community reveals that prolonged exposure to high concentrations of heavy metals, nitric acid and organic solvents (~;;50 years) have resulted in a massive decrease in species and allelic diversity as well as a significant loss of metabolic diversity. Although the surviving microbial community possesses all metabolic pathways necessary for survival and growth in such an extreme environment, its structure is very simple, primarily composed of clonal denitrifying ?- and ?-proteobacterial populations. The resulting community is over-abundant in key genes conferring resistance to specific stresses including nitrate, heavy metals and acetone. Evolutionary analysis indicates that lateral gene transfer could be a key mechanism in rapidly responding and adapting to environmental contamination. The results presented in this study have important implications in understanding, assessing and predicting the impacts of human-induced activities on microbial communities ranging from human health to agriculture to environmental management, and their responses to environmental changes.

Metagenomic Insights into Evolution of a Heavy Metal-Contaminated Groundwater Microbial Community

Speciation of heavy metals in soils and their immobilization at micro-scale interfaces among diverse soil components.

Diversity and composition of soil Acidobacteria and Proteobacteria communities as a bacterial indicator of past land-use change from forest to farmland.

Heavy metal pollution affected the stability and function of soil ecosystem. The impact of heavy metals on soil microbial community and the interaction of microbial community has been widely studied, but little was known about the response of community assembly to the heavy metal pollution. In this study, we collected 30 soil samples from non (CON), moderately (CL) and severely (CH) contaminated fields. The prokaryotic community was studied using high-throughput Illumina sequencing of 16s rRNA gene amplicons, and community assembly were quantified using phylogenetic-bin-based null approach (iCAMP). Results showed that diversity and composition of both bacterial and archaeal community changed significantly in response to heavy metal pollution. The microbial community assembly tended to be more deterministic with the increase of heavy metal concentration. Among the assembly processes, the relative importance of homogeneous selection (deterministic process) increased significantly (increased by 16.2%), and the relative importance of drift and dispersal limitation (stochastic process) decreased significantly (decreased by 11.4% and 5.4%, respectively). The determinacy of bacterial and archaeal community assembly also increased with heavy metal stress, but the assembly models were different. The deterministic proportion of microorganisms tolerant to heavy metals, such as Thiobacillus, Euryarchaeota and Crenarchaeota (clustered in bin 32, bin59 and bin60, respectively) increased, while the stochastic proportion of microorganisms sensitive to heavy metals, such as Koribacteraceae (clustered in bin23) increased. Therefore, the heavy metal stress made the prokaryotic community be deterministic, however, the effects on the assembly process of different microbial groups differed obviously. 

Soil microbial community assembly model in response to heavy metal pollution.

Cleaner technologies to combat heavy metal toxicity

Heavy metal(loid)s exert selective pressure on microbial communities and evolution of metal resistance determinants. Despite increasing knowledge concerning the impact of metal pollution on microbial community and ecological function, it is still a challenge to identify a consistent pattern of microbial community composition along gradients of elevated metal(loid)s in natural environments. Further, our current knowledge of the microbial metal resistome at the community level has been lagging behind compared to the state-of-the-art genetic profiling of bacterial metal resistance mechanisms in a pure culture system. This review provides an overview of the core metal resistant microbiome, development of metal resistance strategies, and potential factors driving the diversity and distribution of metal resistance determinants in natural environments. The impacts of biotic factors regulating the bacterial metal resistome are highlighted. We finally discuss the advances in multiple technologies, research challenges, and future directions to better understand the interface of the environmental microbiome with the metal resistome. This review aims to highlight the diversity and wide distribution of heavy metal(loid)s and their corresponding resistance determinants, helping to better understand the resistance strategy at the community level.

Ying Liu

Papers

Recent advances in exploring the heavy metal(loid) resistant microbiome.