Comparative metagenomics study reveals pollution induced changes of microbial genes in mangrove sediments

Abstract

Mangrove forests are widespread along the subtropical and tropical coasts. They provide a habitat for a wide variety of plants, animals and microorganisms, and act as a buffer zone between the ocean and land. Along with other coastal environments, mangrove ecosystems are under increasing pressure from human activities, such as excessive input of nutrients and toxic pollutants. Despite efforts to understand the diversity of microbes in mangrove sediments, their metabolic capability in pristine and contaminated mangrove sediments remains largely unknown. By using metagenomic approach, we investigated the metabolic capacity of microorganisms in contaminated (CMS) and pristine (PMS) mangrove sediments at subtropical and tropical coastal sites. When comparing the CMS with PMS, we found that the former had a reduced diazotroph abundance and nitrogen fixing capability, but an enhanced metabolism that is related to the generation of microbial greenhouse gases via increased methanogenesis and sulfate reduction. In addition, a high concentration of heavy metals (mainly Zn, Cd, and Pb) and abundance of metal/antibiotic resistance encoding genes were found in CMS. Together, these data provide evidence that contamination in mangrove sediment can markedly change microbial community and metabolism; however, no significant differences in gene distribution were found between the subtropical and tropical mangrove sediments. In summary, contamination in mangrove sediments might weaken the microbial metabolisms that enable the mangrove ecosystems to act as a buffer zone for terrestrial nutrients deposition, and induce bioremediation processes accompanied with an increase in greenhouse gas emission.

Microbial functional signature in the atmospheric boundary layer

“…These specific signatures are thought to result from microbial adaptation and/or physical selection to the environmental abiotic conditions (Hindré et al, 2012;Li et al, 2019;Rey et al, 2016) and are a reflection of the high relative abundances of genes coding for specific functions essential for microorganisms to survive and develop in these environments. For example, microbial metagenomes of human feces were characterized by high relative abundances of sequences annotated as beta-glucosidases that are associated with high intestinal concentrations of complex glycosides; and microbial metagenomes of oceans were enriched in sequences annotated as enzymes catalyzing DMSP (dimethylsulfoniopropionate), that is an organosulfur compound produced by phytoplankton (Delmont et al, 2011).…”

“…However, to our knowledge, only five metagenomic studies on airborne microbial communities at one or two specific sites per study exist (Aalismail et al, 2019;Amato et al, 2019;Cao et al, 2014;Gusareva et al, 2019;Yooseph et al, 2013). Metagenomic investigations of complex microbial communities in many ecosystems (for example, soil, seawater, lakes, feces, sludge) have provided evidence that microorganism functional signatures reflect the abiotic conditions of their environment, with different relative abundances of specific microbial functional classes (Delmont et al, 2011;Li et al, 2019;Tringe et al, 2005;Xie et al, 2011). This observed correlation of microbial community functional potential and the physical and chemical characteristics of their environments could have resulted from genetic modifications (microbial adaptation) (Brune et al, 2000;Hindré et al, 2012;Rey et al, 2016;Yooseph et al, 2010) and/or physical selection.…”

Comparative metagenomics reveals the microbial diversity and metabolic potentials in the sediments and surrounding seawaters of Qinhuangdao mariculture area

“…Metagenomics was also applied to study the upper and core regions of oxygen minimum zones in Arabian Sea, and confirmed the genomic potentials of active nitrogen cycle [19]. The metagenomic results revealed that the metabolic capacity of microorganisms might be weaken by contamination in mangrove sediments and the increase of greenhouse gas emission might be induced [20]. Recently, combining of 16S rRNA amplicon sequencing and metagenomic shotgun analysis revealed that chemical pollutants severely affected microbial structures and functions in sediments [21].…”

Alternativas microbiológicas para la remediación de suelos y aguas contaminados con fertilizantes nitrogenados

“…Por otra parte, estudios como el de Li et al [28] han comprobado que al comparar la capacidad metabólica de los microorganismos presentes en ecosistemas contaminados con fertilizantes y sin contaminar, estos presentan reducción en el pool de genes que les proveen la capacidad de fijar Nitrógeno, mientras que muestran un metabolismo aumentado respecto a la generación de gases de efecto invernadero como el metano o los sulfatos, lo que evidencia cambios en las comunidades y el metabolismo microbiano a causa de este tipo de contaminantes. Fig.…”