Elevated nitrate enriches microbial functional genes for potential bioremediation of complexly contaminated sediments

Interconnection of Key Microbial Functional Genes for Enhanced Benzo[a]pyrene Biodegradation in Sediments by Microbial Electrochemistry

Sediment microbial fuel cells (SMFCs) can stimulate the degradation of polycyclic aromatic hydrocarbons in sediments, but the mechanism of this process is poorly understood at the microbial functional gene level. Here, the use of SMFC resulted in 92% benzo[a]pyrene (BaP) removal over 970 days relative to 54% in the controls. Sediment functions, microbial community structure, and network interactions were dramatically altered by the SMFC employment. Functional gene analysis showed that c-type cytochrome genes for electron transfer, aromatic degradation genes, and extracellular ligninolytic enzymes involved in lignin degradation were significantly enriched in bulk sediments during SMFC operation. Correspondingly, chemical analysis of the system showed that these genetic changes resulted in increases in the levels of easily oxidizable organic carbon and humic acids which may have resulted in increased BaP bioavailability and increased degradation rates. Tracking microbial functional genes and corresponding organic matter responses should aid mechanistic understanding of BaP enhanced biodegradation by microbial electrochemistry and development of sustainable bioremediation strategies.

Divergent taxonomic and functional responses of microbial communities to field simulation of aeolian soil erosion and deposition

Aeolian soil erosion and deposition have worldwide impacts on agriculture, air quality and public health. However, ecosystem responses to soil erosion and deposition remain largely unclear in regard to microorganisms, which are the crucial drivers of biogeochemical cycles. Using integrated metagenomics technologies, we analysed microbial communities subjected to simulated soil erosion and deposition in a semiarid grassland of Inner Mongolia, China. As expected, soil total organic carbon and plant coverage were decreased by soil erosion, and soil dissolved organic carbon (DOC) was increased by soil deposition, demonstrating that field simulation was reliable. Soil microbial communities were altered (p < .039) by both soil erosion and deposition, with dramatic increase in Cyanobacteria related to increased stability in soil aggregates. amyA genes encoding α-amylases were specifically increased (p = .01) by soil deposition and positively correlated (p = .02) to DOC, which likely explained changes in DOC. Surprisingly, most of microbial functional genes associated with carbon, nitrogen, phosphorus and potassium cycling were decreased or unaltered by both erosion and deposition, probably arising from acceleration of organic matter mineralization. These divergent responses support the necessity to include microbial components in evaluating ecological consequences. Furthermore, Mantel tests showed strong, significant correlations between soil nutrients and functional structure but not taxonomic structure, demonstrating close relevance of microbial function traits to nutrient cycling.

The Biogeographic Pattern of Microbial Functional Genes along an Altitudinal Gradient of the Tibetan Pasture

As the highest place of the world, the Tibetan plateau is a fragile ecosystem. Given the importance of microbial communities in driving soil nutrient cycling, it is of interest to document the microbial biogeographic pattern here. We adopted a microarray-based tool named GeoChip 4.0 to investigate grassland microbial functional genes along an elevation gradient from 3200 to 3800 m above sea level open to free grazing by local herdsmen and wild animals. Interestingly, microbial functional diversities increase with elevation, so does the relative abundances of genes associated with carbon degradation, nitrogen cycling, methane production, cold shock and oxygen limitation. The range of Shannon diversities (10.27–10.58) showed considerably smaller variation than what was previously observed at ungrazed sites nearby (9.95–10.65), suggesting the important role of livestock grazing on microbial diversities. Closer examination showed that the dissimilarity of microbial community at our study sites increased with elevations, revealing an elevation-decay relationship of microbial functional genes. Both microbial functional diversity and the number of unique genes increased with elevations. Furthermore, we detected a tight linkage of greenhouse gas (CO₂) and relative abundances of carbon cycling genes. Our biogeographic study provides insights on microbial functional diversity and soil biogeochemical cycling in Tibetan pastures.

Biotechnological Advances for Restoring Degraded Land for Sustainable Development

Global land resources are under severe threat due to pollution and unsustainable land use practices. Restoring degraded land is imperative for regaining ecosystem services, such as biodiversity maintenance and nutrient and water cycling, and to meet the food, feed, fuel, and fibre requirements of present and future generations. While bioremediation is acknowledged as a promising technology for restoring polluted and degraded lands, its field potential is limited for various reasons. However, recent biotechnological advancements, including producing efficient microbial consortia, applying enzymes with higher degrees of specificity, and designing plants with specific microbial partners, are opening new prospects in remediation technology. This review provides insights into such promising ways to harness biotechnology as ecofriendly methods for remediation and restoration.

Temperature response of sulfide/ferrous oxidation and microbial community in anoxic sediments treated with calcium nitrate addition

Nitrate-driven sulfide oxidation has been proved a cost-effective way to control sediments odor which has long been a universal problem for urban rivers in south China areas. In this work, sediments treatment experiments under a dynamic variation of temperature from 5 °C to 35 °C with 3% of calcium nitrate added were conducted to reveal the influence of temperature variation on this process. The results showed that microbial community was remarkably restructured by temperature variation. Pseudomonas (15.56-29.31%), Sulfurimonas (26.81%) and Thiobacillus (37.99%) were dominant genus at temperature of ≤15 °C, 25 °C and 35 °C, respectively. It seemed that species enrichment occurring at different temperature gradient resulted in the distinct variation of microbial community structure and diversity. Moreover, nitrate-driven sulfide and ferrous oxidation were proportionally promoted only when temperature increased above 15 °C. The dominant bacteria at high temperature stage were those genus that closely related to autotrophic nitrate-driven sulfide and ferrous oxidizing bacteria (e.g.Thiobacillus, Sulfurimonas and Thermomonas), revealing that promotion of sulfide/ferrous oxidation could be attributed to the change of dominant bacteria determined by temperature variation. Thus, a higher treatment efficiency by calcium nitrate addition for odor control would be achieved in summer than any other seasons in south China areas.

Functional Characterization of a Novel Amidase Involved in Biotransformation of Triclocarban and its Dehalogenated Congeners in Ochrobactrum sp. TCC-2

Haloaromatic antimicrobial triclocarban (3,4,4'-trichlorocarbanilide, TCC) is a refractory contaminant which is frequently detected in various aquatic and sediment environments globally. However, few TCC-degrading communities or pure cultures have been documented, and functional enzymes involved in TCC biodegradation hitherto have not yet been characterized. In this study, a bacterial strain, Ochrobactrum sp. TCC-2, capable of degrading TCC under both aerobic and anaerobic conditions was isolated from a sediment sample. A novel amidase gene (tccA), responsible for the hydrolysis of the two amide bonds of TCC and its dehalogenated congeners 4,4'-dichlorocarbanilide (DCC) and carbanilide (NCC) to more biodegradable chloroaniline or aniline products, was cloned and characterized. TccA shares low amino acid sequence identity (27 to 38%) with other biochemically characterized amidases and contains the conserved catalytic triad (Ser-Ser-Lys) of the amidase signature enzyme family. TccA was stable over a pH range of 5.0 to 10.0 and at temperatures lower than 60 °C, and it was constitutively expressed in strain TCC-2. In contrast to the halogenated TCC and DCC, the nonchlorinated NCC was the preferred substrate for TccA. TccA also had hydrolysis activity to a broad spectrum of amide bonds in herbicides, insecticides, and chemical intermediates. The constitutive expression and broad substrate spectrum of TccA suggested strain TCC-2 may be potentially useful for bioremediation applications.

Insight of Proteomics and Genomics in Environmental Bioremediation

Bioremediation of hazardous substances from environment is a major human and environmental health concern but can be managed by the microorganism due to their variety of properties that can effectively change the complexity. Microorganisms convey endogenous genetic, biochemical and physiological assets that make them superlative proxies for pollutant remediation in habitat. But, the crucial step is to degrade the complex ring structured pollutants. Interestingly, the integration of genomics and proteomics technologies that allow us to use or alter the genes and proteins of interest in a given microorganism towards a cell-free bioremediation approach. Resultantly, efforts have been finished by developing the genetically modified (Gm) microbes for the remediation of ecological contaminants. Gm microorganisms mediated bioremediation can affect the solubility, bioavailability and mobility of complex hazardous.

Chemical treatment of contaminated sediment for phosphorus control and subsequent effects on ammonia-oxidizing and ammonia-denitrifying microorganisms and on submerged macrophyte revegetation

In this work, sediments were treated with calcium nitrate, aluminum sulfate, ferric sulfate, and Phoslock®, respectively. The impact of treatments on internal phosphorus release, the abundance of nitrogen cycle-related functional genes, and the growth of submerged macrophytes were investigated. All treatments reduced total phosphorus (TP) and soluble reactive phosphorus (SRP) in interstitial water, and aluminum sulfate was most efficient. Aluminum sulfate also decreased TP and SRP in overlying water. Treatments significantly changed P speciations in the sediment. Phoslock® transformed other P species into calcium-bound P. Calcium nitrate, ferric sulfate, and Phoslock® had negative influence on ammonia oxidizers, while four chemicals had positive influence on denitrifies, indicating that chemical treatment could inhibit nitrification but enhance denitrification. Aluminum sulfate had decreased chlorophyll content of the leaves of submerged macrophytes, while ferric sulfate and Phoslock® treatment would inhibit the growth of the root. Based on the results that we obtained, we emphasized that before application of chemical treatment, the effects on submerged macrophyte revegetation should be taken into consideration.

Effects of four different phosphorus-locking materials on sediment and water quality in Xi'an moat

To lower phosphorus concentration in Xi'an moat, four different phosphorus-locking materials, namely, calcium nitrate, sponge-iron, fly ash, and silica alumina clay, were selected in this experiment to study their effects on water quality and sediment. Results of the continuous 68-day experiment showed that calcium nitrate was the most effective for controlling phosphorus concentration in overlying and interstitial water, where the efficiency of locking phosphorus was >97 and 90 %, respectively. Meanwhile, the addition of calcium nitrate caused Fe/Al-bound phosphorus (Fe/Al-P) content in sediment declining but Ca-bound phosphorus (Ca-P) and organic phosphorus (OP) content ascending. The phosphorus-locking efficiency of sponge-iron in overlying and interstitial water was >72 and 66 %, respectively. Meanwhile, the total phosphorus (TP), OP, Fe/Al-P, and Ca-P content in sediment increased by 33.8, 7.7, 23.1, and 23.1 %, respectively, implying that under the action of sponge-iron, the locked phosphorus in sediment was mainly inorganic form and the phosphorus-locking efficiency of sponge-iron could be stable and persistent. In addition, the phosphorus-locking efficiency of fly ash was transient and limited, let alone silica alumina clay had almost no capacity for phosphorus-locking efficiency. Therefore, calcium nitrate and sponge-iron were excellent phosphorus-locking agents to repair the seriously polluted water derived from an internal source.

Insights into the fluoride-resistant regulation mechanism of Acidithiobacillus ferrooxidans ATCC 23270 based on whole genome microarrays

Acidophilic microorganisms involved in uranium bioleaching are usually suppressed by dissolved fluoride ions, eventually leading to reduced leaching efficiency. However, little is known about the regulation mechanisms of microbial resistance to fluoride. In this study, the resistance of Acidithiobacillus ferrooxidans ATCC 23270 to fluoride was investigated by detecting bacterial growth fluctuations and ferrous or sulfur oxidation. To explore the regulation mechanism, a whole genome microarray was used to profile the genome-wide expression. The fluoride tolerance of A. ferrooxidans cultured in the presence of FeSO4 was better than that cultured with the S(0) substrate. The differentially expressed gene categories closely related to fluoride tolerance included those involved in energy metabolism, cellular processes, protein synthesis, transport, the cell envelope, and binding proteins. This study highlights that the cellular ferrous oxidation ability was enhanced at the lower fluoride concentrations. An overview of the cellular regulation mechanisms of extremophiles to fluoride resistance is discussed.

Identifying the key taxonomic categories that characterize microbial community diversity using full-scale classification: a case study of microbial communities in the sediments of Hangzhou Bay

Coastal areas are land-sea transitional zones with complex natural and anthropogenic disturbances. Microorganisms in coastal sediments adapt to such disturbances both individually and as a community. The microbial community structure changes spatially and temporally under environmental stress. In this study, we investigated the microbial community structure in the sediments of Hangzhou Bay, a seriously polluted bay in China. In order to identify the roles and contribution of all microbial taxa, we set thresholds as 0.1% for rare taxa and 1% for abundant taxa, and classified all operational taxonomic units into six exclusive categories based on their abundance. The results showed that the key taxa in differentiating the communities are abundant taxa (AT), conditionally abundant taxa (CAT), and conditionally rare or abundant taxa (CRAT). A large population in conditionally rare taxa (CRT) made this category collectively significant in differentiating the communities. Both bacteria and archaea demonstrated a distance decay pattern of community similarity in the bay, and this pattern was strengthened by rare taxa, CRT and CRAT, but weakened by AT and CAT. This implied that the low abundance taxa were more deterministically distributed, while the high abundance taxa were more ubiquitously distributed.

Impacts of human activities on distribution of sulfate-reducing prokaryotes and antibiotic resistance genes in marine coastal sediments of Hong Kong

Sulfate-reducing prokaryotes (SRPs) and antibiotic resistance genes (ARGs) in sediments could be biomarkers for evaluating the environmental impacts of human activities, although factors governing their distribution are not clear yet. By using metagenomic approach, this study investigated the distributions of SRPs and ARGs in marine sediments collected from 12 different coastal locations of Hong Kong, which exhibited different pollution levels and were classified into two groups based on sediment parameters. Our results showed that relative abundances of major SRP genera to total prokaryotes were consistently lower in the more seriously polluted sediments (P-value < 0.05 in 13 of 20 genera), indicating that the relative abundance of SRPs is a negatively correlated biomarker for evaluating human impacts. Moreover, a unimodel distribution pattern for SRPs along with the pollution gradient was observed. Although total ARGs were enriched in sediments from the polluted sites, distribution of single major ARG types could be explained neither by individual sediment parameters nor by corresponding concentration of antibiotics. It supports the hypothesis that the persistence of ARGs in sediments may not need the selection of antibiotics. In summary, our study provided important hints of the niche differentiation of SRPs and behavior of ARGs in marine coastal sediment.

Short-term enhancement effect of nitrogen addition on microbial degradation and plant uptake of polybrominated diphenyl ethers (PBDEs) in contaminated mangrove soil

Effects of nitrogen (N) addition on the microbial degradation and uptake of a mixture of BDE-47 and -209 by Aegiceras corniculatum, a typical mangrove plant species were investigated. At the end of 3-month experiment, a significant dissipation of BDE-47 was observed in the planted soil, and this dissipation, particularly in rhizosphere soil, was significantly accelerated by the frequent addition of N in the form of ammonium chloride. The removal percentage of BDE-47 in the rhizosphere soil without N addition was 47.3% and increased to 58.2% with N. However, the unplanted soil only removed less than 25% BDE-47, irrespective to N supply. The N addition in planted treatments significantly increased soil N content, urease and dehydrogenase activities, and the abundances of total bacteria and dehalogenating bacteria, leading to more microbial degradation of BDE-47. The N addition also enhanced the root uptake and translocation of PBDEs to above-ground tissues of A. corniculatum. These results suggested that N addition could enhance the phytoremediation of BDE-47-contaminated soil within a short period of time. Different from BDE-47, BDE-209 in all contaminated soils was difficult to be removed due to its persistence and low bioavailability.

Responses of Aromatic-Degrading Microbial Communities to Elevated Nitrate in Sediments

A high number of aromatic compounds that have been released into aquatic ecosystems have accumulated in sediment because of their low solubility and high hydrophobicity, causing significant hazards to the environment and human health. Since nitrate is an essential nitrogen component and a more thermodynamically favorable electron acceptor for anaerobic respiration, nitrate-based bioremediation has been applied to aromatic-contaminated sediments. However, few studies have focused on the response of aromatic-degrading microbial communities to nitrate addition in anaerobic sediments. Here we hypothesized that high nitrate inputs would stimulate aromatic-degrading microbial communities and their associated degrading processes, thus increasing the bioremediation efficiency in aromatic compound-contaminated sediments. We analyzed the changes of key aromatic-degrading genes in the sediment samples from a field-scale site for in situ bioremediation of an aromatic-contaminated creek in the Pearl River Delta before and after nitrate injection using a functional gene array. Our results showed that the genes involved in the degradation of several kinds of aromatic compounds were significantly enriched after nitrate injection, especially those encoding enzymes for central catabolic pathways of aromatic compound degradation, and most of the enriched genes were derived from nitrate-reducing microorganisms, possibly accelerating bioremediation of aromatic-contaminated sediments. The sediment nitrate concentration was found to be the predominant factor shaping the aromatic-degrading microbial communities. This study provides new insights into our understanding of the influences of nitrate addition on aromatic-degrading microbial communities in sediments.

Sediment microbial fuel cell prefers to degrade organic chemicals with higher polarity

By operating a SMFC in heavily contaminated sediment and analyzing its global organic chemical degradation profile, this study showed a brief trend that SMFC prefers to stimulate the degradation of organic chemicals with higher polarity. As a comparison, adding nitrate as a microbial respiration-based sediment remediation strategy preferred lower polarity chemicals. Both SMFC and nitrate reactors showed high degradation capacity in benzene homologs. These results provide crucial information for the selective and proper application of SMFC in bioremediation.

Enhancing the bioremediation by harvesting electricity from the heavily contaminated sediments

To test the long-term applicability of scaled-up sediment microbial fuel cells (SMFCs) in simultaneous bioremediation of toxic-contaminated sediments and power-supply for electronic devices, a 100 L SMFC inoculate with heavily contaminated sediments has been assembled and operated for over 2 years without external electron donor addition. The total organic chemical (TOC) degradation efficiency was 22.1% in the electricity generating SMFCs, which is significantly higher than that in the open-circuited SMFC (3.8%). The organic matters including contaminants in the contaminated sediments were sufficient for the electricity generation of SMFCs, even up to 8.5 years by the present SMFC theoretically. By using a power management system (PMS), the SMFC electricity could be harvested into batteries and used by commercial electronic devices. The results indicated that the SMFC-PMS system could be applied as a long-term and effective tool to simultaneously stimulate the bioremediation of the contaminated sediments and supply power for commercial devices.

Electron acceptor-dependent respiratory and physiological stratifications in biofilms

Bacterial respiration is an essential driving force in biogeochemical cycling and bioremediation processes. Electron acceptors respired by bacteria often have solid and soluble forms that typically coexist in the environment. It is important to understand how sessile bacteria attached to solid electron acceptors respond to ambient soluble alternative electron acceptors. Microbial fuel cells (MFCs) provide a useful tool to investigate this interaction. In MFCs with Shewanella decolorationis, azo dye was used as an alternative electron acceptor in the anode chamber. Different respiration patterns were observed for biofilm and planktonic cells, with planktonic cells preferred to respire with azo dye while biofilm cells respired with both the anode and azo dye. The additional azo respiration dissipated the proton accumulation within the anode biofilm. There was a large redox potential gap between the biofilms and anode surface. Changing cathodic conditions caused immediate effects on the anode potential but not on the biofilm potential. Biofilm viability showed an inverse and respiration-dependent profile when respiring with only the anode or azo dye and was enhanced when respiring with both simultaneously. These results provide new insights into the bacterial respiration strategies in environments containing multiple electron acceptors and support an electron-hopping mechanism within Shewanella electrode-respiring biofilms.