Yuyin Yang

Nonylphenol biodegradation in river sediment and associated shifts in community structures of bacteria and ammonia-oxidizing microorganisms.

Nonylphenol (NP) is one of commonly detected contaminants in the environment. Biological degradation is mainly responsible for remediation of NP-contaminated site. Knowledge about the structure of NP-degrading microbial community is still very limited. Microcosms were constructed to investigate the structure of microbial community in NP-contaminated river sediment and its change with NP biodegradation. A high level of NP was significantly dissipated in 6-9 days. Bacteria and ammonia-oxidizing archaea (AOA) were more responsive to NP amendment compared to ammonia-oxidizing bacteria (AOB). Gammaproteobacteria, Alphaproteobacteria and Bacteroidetes were the largest bacterial groups in NP-degrading sediment. Microorganisms from bacterial genera Brevundimonas, Flavobacterium, Lysobacter and Rhodobacter might be involved in NP degradation in river sediment. This study provides some new insights towards NP biodegradation and microbial ecology in NP-contaminated environment.

Spatiotemporal variation of planktonic and sediment bacterial assemblages in two plateau freshwater lakes at different trophic status

Both planktonic and sediment bacterial assemblages are the important components of freshwater lake ecosystems. However, their spatiotemporal shift and the driving forces remain still elusive. Eutrotrophic Dianchi Lake and mesotrophic Erhai Lake are the largest two freshwater lakes on the Yunnan Plateau (southwestern China). The present study investigated the spatiotemporal shift in both planktonic and sediment bacterial populations in these two plateau freshwater lakes at different trophic status. For either lake, both water and sediment samples were collected from six sampling locations in spring and summer. Bacterioplankton community abundance in Dianchi Lake generally far outnumbered that in Erhai Lake. Sediment bacterial communities in Erhai Lake were found to have higher richness and diversity than those in Dianchi Lake. Sediments had higher bacterial community richness and diversity than waters. The change patterns for both planktonic and sediment bacterial communities were lake-specific and season-specific. Either planktonic or sediment bacterial community structure showed a distinct difference between in Dianchi Lake and in Erhai Lake, and an evident structure difference was also found between planktonic and sediment bacterial communities in either of these two lakes. Planktonic bacterial communities in both Dianchi Lake and Erhai Lake mainly included Proteobacteria (mainly Alpha-, Beta-, and Gammaproteobacteria), Bacteroidetes, Actinobacteria, Cyanobacteria, and Firmicutes, while sediment bacterial communities were mainly represented by Proteobacteria (mainly Beta- and Deltaproteobacteria), Bacteroidetes, Chlorobi, Nitrospirae, Acidobacteria, and Chloroflexi. Trophic status could play important roles in shaping both planktonic and sediment bacterial communities in freshwater lakes.

Abundance and diversity of soil petroleum hydrocarbon-degrading microbial communities in oil exploring areas

Alkanes and polycyclic aromatic hydrocarbons (PAHs) are the commonly detected petroleum hydrocarbon contaminants in soils in oil exploring areas. Hydrocarbon-degrading genes are useful biomarks for estimation of the bioremediation potential of contaminated sites. However, the links between environmental factors and the distribution of alkane and PAH metabolic genes still remain largely unclear. The present study investigated the abundances and diversities of soil n-alkane and PAH-degrading bacterial communities targeting both alkB and nah genes in two oil exploring areas at different geographic regions. A large variation in the abundances and diversities of alkB and nah genes occurred in the studied soil samples. Various environmental variables regulated the spatial distribution of soil alkane and PAH metabolic genes, dependent on geographic location. The soil alkane-degrading bacterial communities in oil exploring areas mainly consisted of Pedobacter, Mycobacterium, and unknown alkB-harboring microorganisms. Moreover, the novel PAH-degraders predominated in nah gene clone libraries from soils of the two oil exploring areas. This work could provide some new insights towards the distribution of hydrocarbon-degrading microorganisms and their biodegradation potential in soil ecosystems.

Distribution of Naphthalene Dioxygenase Genes in Crude Oil-Contaminated Soils

Polycyclic aromatic hydrocarbons (PAHs) are one of the major pollutants in soils in oil exploring areas. Biodegradation is the major process for natural elimination of PAHs from contaminated soils. Functional genes can be used as biomarkers to assess the biodegradation potential of indigenous microbial populations. However, little is known about the distribution of PAH-degrading genes in the environment. The links between environmental parameters and the distribution of PAH metabolic genes remain essentially unclear. The present study investigated the abundance and diversity of naphthalene dioxygenase genes in the oil-contaminated soils in the Shengli Oil Field (China). Spatial variations in the density and diversity of naphthalene dioxygenase genes occurred in this area. Four different sequence genotypes were observed in the contaminated soils, with the predominance of novel PAH-degrading genes. Pearson’s correlation analysis illustrated that gene abundance had positive correlations with the levels of total organic carbon and aromatic hydrocarbons, while gene diversity showed a negative correlation with the level of polar aromatics. This work could provide some new insights toward the distribution of PAH metabolic genes and PAH biodegradation potential in oil-contaminated ecosystems.

Ammonia- and methane-oxidizing microorganisms in high-altitude wetland sediments and adjacent agricultural soils

Ammonia oxidation is known to be carried out by ammonia-oxidizing bacteria (AOB) and archaea (AOA), while methanotrophs (methane-oxidizing bacteria (MOB)) play an important role in mitigating methane emissions from the environment. However, the difference of AOA, AOB, and MOB distribution in wetland sediment and adjacent upland soil remains unclear. The present study investigated the abundances and community structures of AOA, AOB, and MOB in sediments of a high-altitude freshwater wetland in Yunnan Province (China) and adjacent agricultural soils. Variations of AOA, AOB, and MOB community sizes and structures were found in water lily-vegetated and Acorus calamus-vegetated sediments and agricultural soils (unflooded rice soil, cabbage soil, and garlic soil and flooded rice soil). AOB community size was higher than AOA in agricultural soils and lily-vegetated sediment, but lower in A. calamus-vegetated sediment. MOB showed a much higher abundance than AOA and AOB. Flooded rice soil had the largest AOA, AOB, and MOB community sizes. Principal coordinate analyses and Jackknife Environment Clusters analyses suggested that unflooded and flooded rice soils had relatively similar AOA, AOB, and MOB structures. Cabbage soil and A. calamus-vegetated sediment had relatively similar AOA and AOB structures, but their MOB structures showed a large difference. Nitrososphaera-like microorganisms were the predominant AOA species in garlic soil but were present with a low abundance in unflooded rice soil and cabbage soil. Nitrosospira-like AOB were dominant in wetland sediments and agricultural soils. Type I MOB Methylocaldum and type II MOB Methylocystis were dominant in wetland sediments and agricultural soils. Moreover, Pearson’s correlation analysis indicated that AOA Shannon diversity was positively correlated with the ratio of organic carbon to nitrogen (p < 0.05). This work could provide some new insights toward ammonia and methane oxidation in soil and wetland sediment ecosystems.

Simazine biodegradation and community structures of ammonia-oxidizing microorganisms in bioaugmented soil: impact of ammonia and nitrate nitrogen sources

The objective of the present study was to investigate the impact of ammonia and nitrate nitrogen sources on simazine biodegradation by Arthrobacter sp. strain SD1 and the community structures of ammonia-oxidizing archaea (AOA) and bacteria (AOB) in non-agricultural soil. Soil microcosms with different treatments were constructed for herbicide biodegradation test. The relative abundance of the strain SD1 and the structures of AOA and AOB communities were assessed using quantitative PCR (q-PCR) and terminal restriction fragment length polymorphism (TRFLP), respectively. The co-existence of two inorganic nitrogen sources (ammonia and nitrate) had certain impact on simazine dissipation by the strain SD1. Bioaugmentation could induce a shift in the community structures of both AOA and AOB, but AOA were more responsive. Nitrogen application had significant impacts on AOA and AOB communities in bioaugmented soils. Moreover, in non-bioaugmented soil, the community structure of AOA, instead of AOB, could be quickly recovered after herbicide application. This study could add some new insights towards the impacts of nitrogen sources on s-triazine bioremediation and ammonia-oxidizing microorganisms in soil ecosystem.

Sediment Ammonia-Oxidizing Microorganisms in Two Plateau Freshwater Lakes at Different Trophic States.

Both ammonia-oxidizing archaea (AOA) and bacteria (AOB) can contribute to ammonia biotransformation in freshwater lake ecosystems. However, the factors shaping the distribution of sediment AOA and AOB in plateau freshwater lake remains unclear. The present study investigated sediment AOA and AOB communities in two freshwater lakes (hypertrophic Dianchi Lake and mesotrophic Erhai Lake) on the Yunnan Plateau (China). A remarkable difference in the abundance, diversity, and composition of sediment AOA and AOB communities was observed between Dianchi Lake and Erhai Lake. AOB usually outnumbered AOA in Dianchi Lake, but AOA showed the dominance in Erhai Lake. Organic matter (OM), total nitrogen (TN), and total phosphorus (TP) might be the key determinants of AOB abundance, while AOA abundance was likely influenced by the ration of OM to TN (C/N). AOA or AOB community structure was found to be relatively similar in the same lake. TN and TP might play important roles in shaping sediment AOA and AOB compositions in Dianchi Lake and Erhai Lake. Moreover, Nitrososphaera-like AOA were detected in Dianchi Lake. Nitrosospira- and Nitrosomonas-like AOB were dominant in Dianchi Lake and Erhai Lake, respectively. Sediment AOA and AOB communities in Dianchi Lake and Erhai Lake were generally regulated by trophic state.

Temporal and Spatial Dynamics of Archaeal Communities in Two Freshwater Lakes at Different Trophic Status.

In either eutrophic Dianchi Lake or mesotrophic Erhai Lake, the abundance, diversity, and structure of archaeaplankton communities in spring were different from those in summer. In summer, archaeaplankton abundance generally decreased in Dianchi Lake but increased in Erhai Lake, while archaeaplankton diversity increased in both lakes. These two lakes had distinct archaeaplankton community structure. Archaeaplankton abundance was influenced by organic content, while trophic status determined archaeaplankton diversity and structure. Moreover, in summer, lake sediment archaeal abundance considerably decreased. Sediment archaeal abundance showed a remarkable spatial change in spring but only a slight one in summer. The evident spatial change of sediment archaeal diversity occurred in both seasons. In Dianchi Lake, sediment archaeal community structure in summer was remarkably different from that in spring. Compared to Erhai Lake, Dianchi Lake had relatively high sediment archaeal abundance but low diversity. These two lakes differed remarkably in sediment archaeal community structure. Trophic status determined sediment archaeal abundance, diversity and structure. Archaeal diversity in sediment was much higher than that in water. Water and sediment habitats differed greatly in archaeal community structure. Euryarchaeota predominated in water column, but showed much lower proportion in sediment. Bathyarchaeota was an important component of sediment archaeal community.

Spatio-temporal Variation of Sediment Methanotrophic Microorganisms in a Large Eutrophic Lake

Aerobic methane-oxidizing bacteria (MOB) play a crucial role in mitigating the methane emission from lake ecosystems to the atmosphere. However, the distribution of methanotrophic community in shallow and eutrophic lake and its influential factors remain essentially unclear. The present study investigated sediment methanotrophic microorganisms at different sites in eutrophic freshwater Dianchi Lake (China) in two different seasons. The abundance, diversity, and structure of sediment methanotrophic community showed a profound spatial and seasonal variation. The pmoA gene copy number in lake sediments ranged from 8.71 ± 0.49 × 104 to 2.09 ± 0.03 × 107 copies per gram of dry sediment. Sediment methanotrophic communities were composed of Methylococcus and Methylobacter (type I methanotrophs) and Methylosinus (type II methanotrophs), while type I MOB usually outnumbered type II MOB. Moreover, ammonia nitrogen was found to be a potential determinant of methanotrophic community structure in Dianchi Lake.

Vertical profiles of water and sediment denitrifiers in two plateau freshwater lakes

The present study investigated the abundance, richness, diversity, and community composition of denitrifiers (based on nirS and nosZ genes) in the stratified water columns and sediments in eutrophic Dianchi Lake and mesotrophic Erhai Lake using quantitative PCR assay and high-throughput sequencing analysis. Both nirS- and nosZ denitrifiers were detected in waters of these two lakes. Surface water showed higher nosZ gene density than bottom water, and Dianchi Lake waters had larger nirS gene abundance than Erhai Lake waters. The abundance of sediment nirS- and nosZ denitrifiers in Dianchi Lake was larger than that in Erhai Lake. nirS richness and diversity and nosZ richness tended to increase with increasing sediment layer depth in both lakes. The distinct structure difference of sediment nirS- and nosZ denitrifier communities was found between in Dianchi Lake and Erhai Lake. These two lakes also differed greatly in water denitrifier community structure. Moreover, phylogenetic analysis indicated the presence of several different groups of nirS- or nosZ denitrifiers in both lakes. The novel nirS denitrifiers were abundant in both Dianchi Lake and Erhai Lake, while most of the obtained nosZ sequences could be affiliated with known genera.