Effect of red clay on diesel bioremediation and soil bacterial community

Incorporating microbial inoculants to reduce nitrogen loss during sludge composting by suppressing denitrification and promoting ammonia assimilation

To address the challenge of increasing nitrogen retention in compost, this study investigated the effects of microbial communities on denitrification and ammonia assimilation during sludge composting by inoculating microbial inoculants. The results showed that the retention rates of total Kjeldahl nitrogen (TKN) and humic acid (HA) in MIs group (with microbial inoculants) were 4.94 % and 18.52 % higher than those in the control group (CK), respectively. Metagenomic analysis showed that Actinobacteria and Proteobacteria were identified as main microorganisms contributing to denitrification and ammonia assimilation. The addition of microbial agents altered the structure of the microbial community, which in turn stimulated the expression of functional genes. During cooling period, the ammonia assimilation genes glnA, gltB and gltD in MIs were 15.98 %, 24.84 % and 32.88 % higher than those in CK, respectively. Canonical correspondence analysis revealed a positive correlation between the dominant bacterial genera from the cooling stage to the maturity stage and the levels of NO3--N, NH4+-N, HA, and TKN contents. NH4+-N was positively correlated with HA, indicating NH4+-N might be incorporated into HA. Heat map and network analyses revealed NH4+-N as a key factor affecting functional genes of denitrification and ammonia assimilation, with Nitrospira identified as the core bacteria in the microbial network. Therefore, the addition of microbial agents could increase nitrogen retention and improve compost product quality.

Coupled effect of porous network and water content on the natural attenuation of diesel in unsaturated soils

The natural attenuation potential of a vadose zone against diesel is critical for optimizing remedial actions and determining groundwater vulnerability to contamination. Here, diesel attenuation in unsaturated soils was systematically examined to develop a qualitative relationship between physical soil properties and the natural attenuation capacity of a vadose zone against diesel. The uniformity coefficient (C_u) and water saturation (S_w, %) were considered as the proxies reflecting the degree of effects by porous network and water content in different soils, respectively. These, in turn, are related to the primary diesel attenuation mechanisms of volatilization and biodegradation. The volatilization of diesel was inversely proportional to C_u and S_w, which could be attributed to effective pore channels facilitating gas transport. Conversely, biodegradation was highly proportional to C_u under unsaturated conditions (S_w = 35-71%), owing to nutrients typically associated with fine soil particles. The microbial community in unsaturated soils was affected by S_w rather than C_u. The overall diesel attenuation including volatilization and biodegradation was optimized at S_w = 35% for all tested soils.

Modified clays alter diversity and respiration profile of microorganisms in long-term hydrocarbon and metal co-contaminated soil

Clays and surfactant‐modified clays (organoclays) are becoming popular as pollutant sorbents due to their high reactivity and low‐cost availability. However, the lack of field testing and data on ecotoxicity limits their application. Considering such aspects, this study assessed the impact of clay amendments to polycyclic aromatic hydrocarbons (PAHs)/cadmium (Cd)‐contaminated soil on microbial respiration profiles (active vs. inactive cells) using redox staining and the relative abundance and diversity of bacteria and archaea. These clay products are bentonite, cationic surfactant‐modified bentonite and palmitic acid‐grafted surfactant‐modified bentonite). After 70 days, the addition of bentonite and its modified forms altered microbial community structure mainly among dominant groups (Actinobacteria, Proteobacteria, Firmicutes and Chloroflexi) with effects varying depending on material loading to soil. Among amendments, fatty acid (palmitic acid) tailored cationic surfactant‐modified bentonite proved to be microbial growth supportive and significantly increased the number of respiration‐active microbial cells by 5% at a low dose of material (e.g. 1%). Even at high dose (5%), the similarity index using operational taxonomic units (OTUs) also indicates that this modified organoclay‐mixed soil provided only slightly different environment than control soil, and therefore, it could offer more biocompatibility than its counterpart organoclay at similar dose (e.g. cationic surfactant‐modified bentonite). This study promotes designing ‘eco‐safe’ clay‐based sorbents for environmental remediation.

Bioremediation of Artificial Diesel-Contaminated Soil Using Bacterial Consortium Immobilized to Plasma-Pretreated Wood Waste

Bioaugmentation is a bioremediation option based on increasing the natural in-situ microbial population that possesses the ability to degrade the contaminating pollutant. In this study, a diesel-degrading consortium was obtained from an oil-contaminated soil. The diesel-degrading consortium was grown on wood waste that was plasma-pretreated. This plasma treatment led to an increase of bacterial attachment and diesel degradation rates. On the 7th day the biofilm viability on the plasma-treated wood waste reached 0.53 ± 0.02 OD 540 nm, compared to the non-treated wood waste which was only 0.34 ± 0.02. Biofilm attached to plasma-treated and untreated wood waste which was inoculated into artificially diesel-contaminated soil (0.15% g/g) achieved a degradation rate of 9.3 mg day-1 and 7.8 mg day-1, respectively. While, in the soil that was inoculated with planktonic bacteria, degradation was only 5.7 mg day-1. Exposing the soil sample to high temperature (50 °C) or to different soil acidity did not influence the degradation rate of the biofilm attached to the plasma-treated wood waste. The two most abundant bacterial distributions at the family level were Xanthomonadaceae and Sphingomonadaceae. To our knowledge, this is the first study that showed the advantages of biofilm attached to plasma-pretreated wood waste for diesel biodegradation in soil.

Remediation of contaminated lands in the Niger Delta, Nigeria: Prospects and challenges

Contamination of the total environment (air, soil, water and biota) by crude oil has become a paramount interest in the Niger Delta region of Nigeria. Studies have revealed variable impacts of oil toxicity on the environment and exposed populations. The revelation gained much international attention in 2011 with the release of Environmental Assessment of Ogoniland report by the United Nations Environment Programme (UNEP). This has up scaled local and international pressures for urgent clean-up and restoration of degraded bio-resource rich environments of the Niger Delta, starting from Ogoniland. Previous remediation attempts in the area had failed due to erroneous operational conclusions (such as conclusions by oil industry operators that the Niger Delta soil is covered by a layer of clay and as such oil percolation remains within the top soil and makes remediation by enhanced natural attenuation (RENA) suitable for the region) and the adoption of incompatible and ineffective approaches (i.e. RENA) for the complex and dynamic environments. Perennial conflicts, poor regulatory oversights and incoherent standards are also challenges. Following UNEP recommendations, the Federal Government of Nigeria recently commissioned the clean-up and remediation of Ogoniland project; it would be novel and trend setting. While UNEP outlined some measures of contaminated land remediation, no specific approach was identified to be most effective for the Niger Delta region. Resolving the technical dilemma and identified social impediments is the key success driver of the above project. In this paper, we reviewed the socio-economic and ecological impacts of contaminated land in the Niger Delta region and the global state-of-the-art remediation approaches. We use coastal environment clean-up case studies to demonstrate the effectiveness of bioremediation (sometimes in combination with other technologies) for remediating most of the polluted sites in the Niger Delta. Bioremediation should primarily be the preferred option considering its low greenhouse gas and environmental footprints, and low-cost burden on the weak and overstretched economy of Nigeria.

Experimental study of clay-hydrocarbon interactions relevant to the biodegradation of the Deepwater Horizon oil from the Gulf of Mexico

Adding clay to marine oil pollution represents a promising approach to enhance bacterial hydrocarbon degradation in nutrient poor waters. In this study, three types of regionally available clays (Ca-bentonite, Fuller's Earth and kaolin) were tested to stimulate the biodegradation of source and weathered oil collected from the Deepwater Horizon spill. The weathered oil showed little biodegradation prior to experimentation and was extensively degraded by bacteria in the laboratory in a similar way as the alkane-rich source oil. For both oils, the addition of natural clay-flakes showed minor enhancement of oil biodegradation compared to the non-clay bearing control, but the clay-oil films did limit evaporation. Only alkanes of a molecular weight (MW) > 420 showed significant reduction by enhanced biodegradation following natural clay treatment. In contrast, all fertilized clay flakes showed major bacterial degradation of the oil, with a 6-10 times reduction in alkane content, and an up to 8 fold increase in the rate of O2 consumption. Compared to the control, such treatment showed particular reduction of longer chained alkanes (MW > 226). The application of natural and fertilized clay flakes also showed selective reduction of PAHs, mainly in the MW range of 200-300, but without significant change in the toxicity indices measured. These results imply that a large variety of clays may be used to boost oil biodegradation by aiding attachment of fertilizing nutrients to the oil.

Yucatán in black and red: Linking edaphic analysis and pyrosequencing-based assessment of bacterial and fungal community structures in the two main kinds of soil of Yucatán State

Yucatán State is dominated by two kinds of soil, named "Black Leptosol" and "Red Leptosol", which are interwoven across the State. In this work, we analyzed the relation between the edaphic characteristics and the bacterial and fungal community structures in these two kinds of Leptosol. The results revealed that Black Leptosol (BlaS) had a higher content of calcium carbonates, organic matter, nitrogen, and phosphorus than Red Leptosol (RedS). The most outstanding difference in the bacterial community structure between BlaS and RedS was that while in BlaS Actinobacteria was the most abundant phylum (43.7%), followed by Acidobacteria (26.9%) and Proteobacteria (23.6%), in RedS the bacterial community was strongly dominated by Acidobacteria (83%). Two fungal phyla were identified in both kinds of soil; Ascomycota, with 77% in BlaS and 56% in RedS, and Basidiomycota, with 22% in RedS and only 0.67% in BlaS. The most relevant difference between the two fungal communities was that excepting for Fusarium sp., all the species they had were different. Thus, in contrast with bacterial communities, where most of the major OTUs were present in both kinds of soil, fungal communities appeared to be unique to each kind of Leptosol.

Metagenomic and functional analyses of the consequences of reduction of bacterial diversity on soil functions and bioremediation in diesel-contaminated microcosms

The relationship between microbial biodiversity and soil function is an important issue in ecology, yet most studies have been performed in pristine ecosystems. Here, we assess the role of microbial diversity in ecological function and remediation strategies in diesel-contaminated soils. Soil microbial diversity was manipulated using a removal by dilution approach and microbial functions were determined using both metagenomic analyses and enzymatic assays. A shift from Proteobacteria- to Actinobacteria-dominant communities was observed when species diversity was reduced. Metagenomic analysis showed that a large proportion of functional gene categories were significantly altered by the reduction in biodiversity. The abundance of genes related to the nitrogen cycle was significantly reduced in the low-diversity community, impairing denitrification. In contrast, the efficiency of diesel biodegradation was increased in the low-diversity community and was further enhanced by addition of red clay as a stimulating agent. Our results suggest that the relationship between microbial diversity and ecological function involves trade-offs among ecological processes, and should not be generalized as a positive, neutral, or negative relationship.

Metagenomic evidence for the presence of phototrophic Gemmatimonadetes bacteria in diverse environments

Gemmatimonadetes represents a poorly understood bacterial phylum with only a handful of cultured species. Recently, one of its few representatives, Gemmatimonas phototrophica, was found to contain purple bacterial photosynthetic reaction centres. However, almost nothing is known about the environmental distribution of phototrophic Gemmatimonadetes bacteria. To fill this gap, we took advantage of fast-growing public metagenomic databases and performed an extensive survey of metagenomes deposited into the NCBI's WGS database, the JGI's IMG webserver and the MG-RAST webserver. By employing Mg protoporphyrin IX monomethyl ester oxidative cyclase (AcsF) as a marker gene, we identified 291 AcsF fragments (24-361 amino acids long) that are closely related to G. phototrophica from 161 metagenomes originating from various habitats, including air, river waters/sediment, estuarine waters, lake waters, biofilms, plant surfaces, intertidal sediment, soils, springs and wastewater treatment plants, but none from marine waters or sediment. Based on AcsF hit counts, phototrophic Gemmatimonadetes bacteria make up 0.4-11.9% of whole phototrophic microbial communities in these habitats. Unexpectedly, an almost complete 37.9 kb long photosynthesis gene cluster with identical gene composition and arrangement to those in G. phototrophica was reconstructed from the Odense wastewater metagenome, only differing in a 7.2 kb long non-photosynthesis-gene insert. These data suggest that phototrophic Gemmatimonadetes bacteria are much more widely distributed in the environment and exhibit a higher genetic diversity than previously thought.

Molecular Mechanisms of Enhanced Bacterial Growth on Hexadecane with Red Clay

Red clay was previously used to enhance bioremediation of diesel-contaminated soil. It was speculated that the enhanced degradation of diesel was due to increased bacterial growth. In this study, we selected Acinetobacter oleivorans DR1, a soil-borne degrader of diesel and alkanes, as a model bacterium and performed transcriptional analysis using RNA sequencing to investigate the cellular response during hexadecane utilization and the mechanism by which red clay promotes hexadecane degradation. We confirmed that red clay promotes the growth of A. oleivorans DR1 on hexadecane, a major component of diesel, as a sole carbon source. Addition of red clay to hexadecane-utilizing DR1 cells highly upregulated β-oxidation, while genes related to alkane oxidation were highly expressed with and without red clay. Red clay also upregulated genes related to oxidative stress defense, such as superoxide dismutase, catalase, and glutaredoxin genes, suggesting that red clay supports the response of DR1 cells to oxidative stress generated during hexadecane utilization. Increased membrane fluidity in the presence of red clay was confirmed by fatty acid methyl ester analysis at different growth phases, suggesting that enhanced growth on hexadecane could be due to increased uptake of hexadecane coupled with upregulation of downstream metabolism and oxidative stress defense. The monitoring of the bacterial community in soil with red clay for a year revealed that red clay stabilized the community structure.