The impact of arbuscular mycorrhizal fungi and endophytic bacteria on peanuts under the combined pollution of cadmium and microplastics

It remains unclear how symbiotic microbes impact the growth of peanuts when they are exposed to the pollutants cadmium (Cd) and microplastics (MPs) simultaneously. This study aimed to investigate the effects of endophytic bacteria Bacillus velezens SC60 and arbuscular mycorrhizal fungus Rhizophagus irregularis on peanut growth and rhizosphere microbial communities in the presence of Cd at 40 (Cd40) or 80 (Cd80) mg kg-1 combined without MP or the presence of low-density polyethylene (LDPE) and poly butyleneadipate-co-terephthalate (PBAT). This study assessed soil indicators, plant parameters, and Cd accumulation indicators. Results showed that the application of R. irregularis and B. velezens significantly enhanced soil organic carbon and increased Cd content under the conditions of Cd80 and MPs co-pollution. R. irregularis and B. velezens treatment increased peanut absorption and the enrichment coefficient for Cd, with predominate concentrations localized in the peanut roots, especially under combined pollution by Cd and MPs. Under treatments with Cd40 and Cd80 combined with PBAT pollution, soil microbes Proteobacteria exhibited a higher relative abundance, while Actinobacteria showed a higher relative abundance under treatments with Cd40 and Cd80 combined with LDPE pollution. In conclusion, under the combined pollution conditions of MPs and Cd, the co-treatment of R. irregularis and B. velezens effectively immobilized Cd in peanut roots, impeding its translocation to the shoot.

Prediction of microbial activity and abundance using interpretable machine learning models in the hyporheic zone of effluent-dominated receiving rivers

Serving as a vital linkage between surface water and groundwater, the hyporheic zone (HZ) plays a fundamental role in improving water quality and maintaining ecological security. In arid or semi-arid areas, effluent discharge from wastewater treatment facilities could occupy a predominant proportion of the total base flow of receiving rivers. Nonetheless the relationship between microbial activity, abundance and environmental factors in the HZ of effluent-receiving rivers appear to be rarely addressed. In this study, a spatiotemporal field study was performed in two representative effluent-dominated receiving rivers in Xi'an, China. Land use data, physical and chemical water quality parameters of surface and subsurface water were used as predictive variables, while the microbial respiratory electron transport system activity (ETSA), the Chao1 and Shannon index of total microbial community, as well as the Chao1 and Shannon index of denitrifying bacteria community were used as response variables, while ETSA was used as response variables indicating ecological processes and Shannon and Chao1 were utilized as parameters indicating microbial diversity. Two machine learning models were utilized to provide evidence-based information on how environmental factors interact and drive microbial activity and abundance in the HZ at variable depths. The models with Chao1 and Shannon as response variables exhibited excellent predictive performances (R2: 0.754-0.81 and 0.783-0.839). Dissolved organic nitrogen (DON) was the most important factor affecting the microbial functions, and an obvious threshold value of ∼2 mg/L was observed. Credible predictions of models with Chao1 and Shannon index of denitrifying bacteria community as response variables were detected (R2: 0.484-0.624 and 0.567-0.638), with soluble reactive phosphorus (SRP) being the key influencing factor. Fe (Ⅱ) was favorable in predicting denitrifying bacteria community. The ESTA model highlighted the importance of total nitrogen in the ecological health monitoring in HZ. These findings provide novel insights in predicting microbial activity and abundance in highly-impacted areas such as the HZ of effluent-dominated receiving rivers.

Using biochar for environmental recovery and boosting the yield of valuable non-food crops: The case of hemp in a soil contaminated by potentially toxic elements (PTEs)

Hemp (Cannabis sativa L.) is known to tolerate high concentrations of soil contaminants which however can limit its biomass yield. On the other hand, organic-based amendments such as biochar can immobilize soil contaminants and assist hemp growth in soils contaminated by potentially toxic elements (PTEs), allowing for environmental recovery and income generation, e.g. due to green energy production from plant biomass. The aim of this study was therefore to evaluate the suitability of a softwood-derived biochar to enhance hemp growth and promote the assisted phytoremediation of a PTE-contaminated soil (i.e., Sb 2175 mg kg-1; Zn 3149 mg kg-1; Pb 403 mg kg-1; and Cd 12 mg kg-1). Adding 3% (w/w) biochar to soil favoured the reduction of soluble and exchangeable PTEs, decreased soil dehydrogenase activity (by ∼2.08-fold), and increased alkaline phosphomonoesterase and urease activities, basal respiration and soil microbial carbon (by ∼1.18-, 1.22-, 1.22-, and 1.66-fold, respectively). Biochar increased the abundance of selected soil culturable microorganisms, while amplicon sequencing analysis showed a positive biochar impact on α-diversity and the induction of structural changes on soil bacterial community structure. Biochar did not affect root growth of hemp but significantly increased its aboveground biomass by ∼1.67-fold for shoots, and by ∼2-fold for both seed number and weight. Biochar increased the PTEs phytostabilisation potential of hemp with respect to Cd, Pb and Zn, and also stimulated hemp phytoextracting capacity with respect to Sb. Overall, the results showed that biochar can boost hemp yield and its phytoremediation effectiveness in soils contaminated by PTEs providing valuable biomass that can generate profit in economic, environmental and sustainability terms.

Environmental impacts on algal-bacterial-based aquaponics system by different types of carbon source addition: water quality and greenhouse gas emission

Carbon source addition is an important way improving the carbon and nitrogen transformation in aquaculture system; however, its effectiveness of algal-bacterial-based aquaponics (AA) through carbon source addition is still vague. In this study, the influences of organic carbon (OC-AA system) and inorganic carbon (IC-AA system) addition and without carbon source addition (C-AA system) on the operational performance of AA system were investigated. Results showed that 10.1-19.5% increase of algal-bacterial biomass enhanced the purifying effect of ammonia nitrogen in OC-AA system and IC-AA system relative to C-AA system. Moreover, extra electron donor supply in the OC-AA system obtained the lowest NO3--N concentration. However, that was at the cost of aggravated N2O conversion ratio, which increased by more than 2.0-folds than other systems, attributing to 2.9-folds increase of nirS gene abundance. In addition, carbon source addition increased the pH and then decreased the fish biomass production of AA system. The results of this study would provide theoretical supports of carbon source addition on the performance of nutrient transformation and greenhouse gas effect in AA system.

An efficient method for high molecular weight bacterial DNA extraction suitable for shotgun metagenomics from skin swabs

The human skin microbiome represents a variety of complex microbial ecosystems that play a key role in host health. Molecular methods to study these communities have been developed but have been largely limited to low-throughput quantification and short amplicon-based sequencing, providing limited functional information about the communities present. Shotgun metagenomic sequencing has emerged as a preferred method for microbiome studies as it provides more comprehensive information about the species/strains present in a niche and the genes they encode. However, the relatively low bacterial biomass of skin, in comparison to other areas such as the gut microbiome, makes obtaining sufficient DNA for shotgun metagenomic sequencing challenging. Here we describe an optimised high-throughput method for extraction of high molecular weight DNA suitable for shotgun metagenomic sequencing. We validated the performance of the extraction method, and analysis pipeline on skin swabs collected from both adults and babies. The pipeline effectively characterised the bacterial skin microbiota with a cost and throughput suitable for larger longitudinal sets of samples. Application of this method will allow greater insights into community compositions and functional capabilities of the skin microbiome.

Machine learning sheds light on physical-chemical and biological parameters leading to Abrolhos coral reef microbialization

Microbes play a central role in coral reef health. However, the relative importance of physical-chemical and biological processes in the control of microbial biomass are unknown. Here, we applied machine learning to analyze a large dataset of biological, physical, and chemical parameters (N = 665 coral reef seawater samples) to understand the factors that modulate microbial abundance in the water of Abrolhos reefs, the largest and richest coral reefs of the Southwest Atlantic. Random Forest (RF) and Boosted Regression Tree (BRT) models indicated that hydrodynamic forcing, Dissolved Organic Carbon (DOC), and Total Nitrogen (TN) were the most important predictors of microbial abundance. The possible cumulative effects of higher temperatures, longer seawater residence time, higher nutrient concentration, and lower coral and fish biomass observed in coastal reefs resulted in higher microbial abundance, potentially impacting coral resilience against stressors.

Synergistic effects of rice husk biochar and aerobic composting for heavy oil-contaminated soil remediation and microbial community succession evaluation

Soil petroleum pollution is an urgent problem in modern society, which seriously threatens the ecological balance and environmental safety. Aerobic composting technology is considered economically acceptable and technologically feasible for the soil remediation. In this study, the combined experiment of aerobic composting with the addition of biochar materials was conducted for the remediation of heavy oil-contaminated soil, and treatments with 0, 5, 10 and 15 wt% biochar dosages were labeled as CK, C5, C10 and C15, respectively. Conventional parameters (temperature, pH, NH₄⁺-N and NO₃^--N) and enzyme activities (urease, cellulase, dehydrogenase and polyphenol oxidase) during the composting process were systematically investigated. Remediation performance and functional microbial community abundance were also characterized. According to experimental consequences, removal efficiencies of CK, C5, C10 and C15 were 48.0%, 68.1%, 72.0% and 73.9%, respectively. The comparison with abiotic treatments corroborated that biostimulation rather than adsorption effect was the main removal mechanism during the biochar-assisted composting process. Noteworthy, the biochar addition regulated the succession process of microbial community and increased the abundance of microorganisms related to petroleum degradation at the genus level. This work demonstrated that aerobic composting with biochar amendment would be a fascinating technology for petroleum-contaminated soil remediation.

Species shifts induce soil organic matter priming and changes in microbial communities

Invasion of plant species with functional traits that influences the rhizosphere can have significant effects on soil organic matter (SOM) dynamics if the invasive species stimulates soil microbial communities with, for example, an enhanced supply of labile carbon and oxygen. We evaluated these effects along a Phragmites invasion chronosequence spanning over 40 years. Using a δ¹³C and δ¹⁵N enriched substrate, we separated SOM-derived and substrate-derived carbon (C) and nitrogen (N) mineralization in surface (top 15 cm), shallow (30-45 cm), and deep (65-80 cm) soils collected from established, newly invaded, and native plant communities. We found all soils were susceptible to SOM priming, but priming profiles differed between vegetation communities, being highest at the surface in native assemblage soils, whereas highest at depth under invasive plants. Changes in functional microbial community composition at depth in Phragmites soils, evidenced by an increase in relative fungal laccase abundance, explained the SOM priming in these deep invaded soils. Our results show that invasive Phragmites maintains a microbial community at depth able to degrade SOM faster than that under native vegetation, evidencing that plant species shifts can fundamentally change soil biogeochemistry, altering element cycling and decreasing SOM residence time. Furthermore, our experimental design allowed to quantify real-time SOM-C and SOM-N gross mineralization, resulting in a new model relating C and N mineralization in these wetland soils and providing new insights on how SOM decomposition impacts N availability and cycling across wetland N pools.

Linking the chemical nature of soil organic carbon and biological binding agent in aggregates to soil aggregate stability following biochar amendment in a rice paddy

Changes in soil aggregation with biochar amendment have been investigated extensively, but how biochar affects the chemical composition of organic carbon (C) and biological binding agents in aggregates and their linkage with soil aggregate stability remains unclear. Soil samples were collected in a rice paddy treated with 0 (C0, control), 10 t ha^-1 (C10), 20 t ha^-1 (C20) and 40 t ha^-1 (C40) biochar for twenty months. The amount and chemical composition of soil organic C (SOC), microbial abundances and glomalin-related soil protein (GRSP) were determined in bulk soil and four fractions: large macroaggregates (>2000 μm), small macroaggregates (250-2000 μm), microaggregates (53-250 μm), and silt + clay (<53 μm). Our results showed that the proportion of >250 μm water-stable aggregates and mean weight diameter were gradually increased with increasing biochar addition rate. The concentrations of SOC, readily oxidizable C and microbial biomass C increased most in the small macroaggregates, followed by microaggregates under biochar amendment. Increasing biochar addition rate gradually decreased the relative contents of alkyl C, O-alkyl C and carbonyl C, but increased those of aromatic C across the aggregates, resulting in a higher aromaticity and hydrophobicity of SOC with respect to the control. The abundances of bacteria, fungi and archaea and the content of GRSP were significantly enhanced in the large and small macroaggregates under the C40 treatment. The proportion of >250 μm aggregates was significantly correlated with the contents of soil organic C fractions, GRSP and microbial abundance. Structural equation modeling further revealed that changes in SOC hydrophobicity and GRSP content under biochar amendment had significant and direct effects on the soil aggregate size distribution. In summary, our findings suggest that biochar amendment in rice paddy could improve soil aggregation through altering the chemical composition of soil organic C and the abundance of biological binding agents.

Biochar amendment of aerobic composting for the effective biodegradation of heavy oil and succession of bacterial community

Soil pollution caused by petroleum pollutants from production trade activities in petroleum-related factories contributes serious threat to the environment and human health. Composting is technically-feasible and cost-effective in the biodegradation of heavy oil pollutants. This composting experiment was developed with four rice husk biochar (RHB) concentrations of 0 wt% (CK), 5 wt% (S1), 10 wt% (S2) and 15 wt% (S3) for the degradation of heavy oil. The results showed that RHB amendment could strengthen the degradation performance of heavy oil, and the degradation efficiencies for CK, S1, S2 and S3 were 59.67%, 65.00%, 73.29% and 74.82%, respectively. Microbial community succession process was investigated through high-throughput sequencing technology, and the RHB addition regulated bacterial community succession and further effectively facilitated the biodegradation of heavy oil in composting. This study substantiated that biochar materials-amended aerobic composting would be a promising strategy for the biodegradation of petroleum pollutants.

Stratification patterns of anammox granular sludge bed: Linking particle size distribution to microbial activity and community

Anammox granular sludge processes are an attractive and efficient biotechnology in the field of wastewater treatment. In this study, the stratification patterns of anammox granular sludge bed (GSB) at steady states were illustrated and its relationship to microbial activity and community were systematically investigated under different nitrogen loading rates (NLRs). Morphological observation and quantitive particle size distribution analysis demonstrated that the GSB at low NLR was mainly composed of micro and fine granules with a big difference between bottom and top sludge layers. But at high NLR, the volumetric mean diameter (VMD) of GSB increased with the size distribution width (Span) declined forming a more homogeneous and coarse granules population. The particle size distribution parameters of GSB could be fast characterized by the optical lightness (L*) parameter (r = -0.771, p < 0.01, n = 16) and held a significant correlation with the nitrogen removal rate (NRR) of anammox system (r > 0.9, p < 0.05). The microbial spatial distribution patterns of different sludge layers were further investigated by high-throughput sequencing. The microbial community α-diversity index and microbial abundance matrix proved that the community structure tend to coverage at high NLR. Significant difference of the relative abundance of microbial community was detected under different NLRs. The VMD of GSB held a significant correlation with the relative abundance of AnAOB (r = 0.556, p < 0.01, n = 16) and other common accompanying bacteria (Denitratisoma and Chloroflexi). This study proved that the apparent particle size distribution patterns of GSB could be a potential auxiliary indicator to reflect the microbial activity and community, which can facilitate the innovative process monitor of anammox system based on visual features.

Functional enrichment of gut microbiome by early supplementation of Bacillus based probiotic in cage free hens: a field study

BACKGROUND

The chicken gut microbiota passes through different stages of maturation; therefore, strengthening it with well characterised probiotics increases its resilience required for optimum gut health and wellbeing. However, there is limited information on the interaction of Bacillus based probiotics with gut microbial community members in cage free laying chickens both in rearing and production phases of life. In the current study, we investigated the changes in the gut microbiome of free range hens in the field after Bacillus based probiotic supplementation.

RESULTS

Overall, at phylum level, probiotic supplementation increased the populations of Bacteroidetes and Proteobacteria mainly at the expense of Firmicutes. The population of Bacteroidetes significantly increased during the production as compared to the rearing phase, and its higher population in the probiotic-supplemented chickens reflects the positive role of Bacillus based probiotic in gut health. Core differences in the beta diversity suggest that probiotic supplementation decreased microbial compositionality. The non-significant difference in alpha diversity between the probiotic and control chickens showed that the composition of community structure did not change. No Salmonella spp. were isolated from the probiotic supplemented birds. Egg internal quality was significantly higher, while egg production and body weight did not differ. Functional prediction data showed that probiotic supplementation enriched metabolic pathways, such as vitamin B6 metabolism, phenylpropanoid biosynthesis, monobactam biosynthesis, RNA degradation, retinol metabolism, pantothenate and CoA biosynthesis, phosphonate and phosphinate metabolism, AMPK signaling pathway, cationic antimicrobial peptide (CAMP) resistance and tyrosine metabolism.

CONCLUSIONS

Overall, age was the main factor affecting the composition and diversity of gut microbiota, where probiotic supplementation improved the abundance of many useful candidates in the gut microbial communities. The generated baseline data in the current study highlights the importance of the continuous use of Bacillus based probiotic for optimum gut health and production.

Machine learning approach identifies water sample source based on microbial abundance

Water quality can change along a river system due to differences in adjacent land use patterns and discharge sources. These variations can induce rapid responses of the aquatic microbial community, which may be an indicator of water quality characteristics. In the current study, we used a random forest model to predict water sample sources from three different river ecosystems along a gradient of anthropogenic disturbance (i.e., less disturbed mountainous area, wastewater discharged urban area, and pesticide and fertilizer applied agricultural area) based on environmental physicochemical indices (PCIs), microbiological indices (MBIs), and their combination. Results showed that among the PCI-based models, using conventional water quality indices as inputs provided markedly better prediction of water sample source than using pharmaceutical and personal care products (PPCPs), and much better prediction than using polycyclic aromatic hydrocarbons (PAHs) and substituted PAHs (SPAHs). Among the MBI-based models, using the abundances of the top 30 bacteria combined with pathogenic antibiotic resistant bacteria (PARB) as inputs achieved the lowest median out-of-bag error rate (9.9%) and increased median kappa coefficient (0.8694), while adding fungal inputs reduced the kappa coefficient. The model based on the top 30 bacteria still showed an advantage compared with models based on PCIs or the combination of PCIs and MBIs. With improvement in sequencing technology and increase in data availability in the future, the proposed method provides an economical, rapid, and reliable way in which to identify water sample sources based on abundance data of microbial communities.

Palmitic acid mediated change of rhizosphere and alleviation of Fusarium wilt disease in watermelon

Palmitic acid (PA) in root exudates or decaying residues can reduce the incidence of soil-borne diseases and promote the growth of some crop plants. However, the effects of PA on soil-borne pathogens and microbial communities are poorly understood. Here, we investigate the effects of PA on overall watermelon microbial communities and the populations of Fusarium oxysporum f.sp. niveum (Fon). The effects of PA on the mycelial growth and spore production of Fon were tested in vitro, while its effects on Fon, total bacteria and total fungi populations, and microbial communities were evaluated in a pot experiment. The results revealed that all test concentrations of PA inhibited Fon mycelia growth and spore production. The pot experiment showed that 0.5 mM and 1 mM PA reduced Fon but increased total bacteria populations, and 0.5 mM and 1 mM PA 0.5 mM and 1 mM PA promoted the change to a soil type of bacteria soil. Meanwhile, 0.5 mM PA and 1 mM PA altered the community composition of the rhizosphere microorganisms and reduced the relative abundance of two bacterial operational taxonomic units (OTUs) and the two fungal OTUs that were significantly (p < 0.01) related with disease severity and increased that of four bacterial OTUs and the two fungal that were highly significantly (p < 0.01) negatively correlated with the disease severity. These results suggest that application of PA decreased the populations of Fon, changed the rhizosphere microbial composition, reduced the disease severity of Fusarium wilt, and promoted the growth of watermelon.

Germination, root elongation, and photosynthetic performance of plants exposed to sodium lauryl ether sulfate (SLES): an emerging contaminant

The anionic surfactant SLES (sodium lauryl ether sulfate) is an emerging contaminant, being the main component of foaming agents that are increasingly used by the tunnel construction industry. To fill the gap of knowledge about the potential SLES toxicity on plants, acute and chronic effects were assessed under controlled conditions. The acute ecotoxicological test was performed on Lepidum sativum L. (cress) and Zea mays L. (maize). Germination of both species was not affected by SLES in soil, even at concentrations (1200 mg kg-1) more than twice higher than the maximum realistic values found in contaminated debris, thus confirming the low acute SLES toxicity on terrestrial plants. The root elongation of the more sensitive species (cress) was instead reduced at the highest SLES concentration. In the chronic phytotoxicity experiment, photosynthesis of maize was downregulated, and the photosynthetic performance (PITOT) significantly reduced already under realistic exposures (360 mg kg-1), owing to the SLES ability to interfere with water and/or nutrients uptake by roots. However, such reduction was transient, likely due to the rapid biodegradation of the surfactant by the soil microbial community. Indeed, SLES amount decreased in soil more than 90% of the initial concentration in only 11 days. A significant reduction of the maximum photosynthetic capacity (Pnmax) was still evident at the end of the experiment, suggesting the persistence of negative SLES effects on plant growth and productivity. Overall results, although confirming the low phytotoxicity and high biodegradability of SLES in natural soils, highlight the importance of considering both acute and nonlethal stress effects to evaluate the environmental compatibility of soil containing SLES residues.

Soil microbial diversity in organic and non-organic pasture systems

Understanding the effects of organic pasture management on the soil microbiome is important for sustainable forage production since soil microbiome diversity contributes to improved nutrient cycling, soil structure, plant growth, and environmental resiliency; however, the soil microbiome response to pasture management is largely unknown. This study assessed the soil microbial diversity, richness, and community structure following 10 years of pasture management (organic or non-organic) of the V4 region of the 16S rRNA using the Illumina MiSeq platform. Soil samples were collected from 0–15 cm in July and August from 2017–2018 and soil nutrient properties (nutrients, carbon, nitrogen, and pH) quantified and correlated with soil microbial diversity. Overall, greater soil bacterial species richness (P ≤ 0.05) occurred in organic relative to non-organic (conventional) systems. Management affected bacterial species richness (Chao1), with greater richness occurring in organic pasture soils and less richness occurring in non-organic systems (P ≤ 0.05). Similarly, management affected bacterial evenness (Simpson’s index), with a more diverse community occurring in organically managed soils relative to non-organic pastures (P ≤ 0.05). Linear discriminant analysis effect size analysis showed statistically significant and biologically consistent differences in bacterial taxa in organic compared with non-organic soils. Therefore, there was a shift in bacterial community structure in organic relative to non-organic soils (P ≤ 0.05). Additionally, soil nutrients (Fe, Mg, Ni, S, Al, K, Cd, and Cu), pH, C, and N were correlated with one or more dominant bacterial phyla (Gemmatimonadetes, Planctomycetes, Firmicutes, Chloroflexi, Actinobacteria, and Acidobacteria). Overall, pasture management affected soil microbial diversity, with greater diversity occurring in organic than non-organic systems, likely owing to applications of organic poultry litter in organic systems compared to non-organic management (use of inorganic-fertilizers and herbicides). Results indicate that when pastures are converted to organic production systems, soil microbial richness and diversity may increase, thereby resulting in enhanced soil microbiome diversity and overall ecosystem services.

Effect of land use on soil properties, microbial abundance and diversity of four different crop lands in central Myanmar

Changing land use systems impact on local edaphic factors and microbial abundance and diversity, however, the information on it in central Myanmar's soils is still lacking. Therefore, soils with four different land uses were analyzed; WAP (soil from perennial tree orchard), PNON (soil from crop rotation of peanut and onion), SESA (soil from mono-crop of sesame) and CHON (soil from mono-crop of onion for 3 years consecutively). Soil organic carbon (SOC), total nitrogen (TN), dissolved organic carbon (DOC), ammonium nitrogen (NH₄ ⁺-N) and pH showed the highest in PNON soil, which suggested crop rotation with high fertilizer input and irrigation had positive effect on the edaphic factors of soil. CHON soil showed the lowest in most soil properties and microbial abundance as a result of intensive use of fertilizer and irrigation, no crop rotation and no input of manures. Microbial community composition showed differences among tested soils and relative abundance of Chloroflexi was the highest in CHON soil whereas that of Basidiomycota was the highest in WAP soil. The abundances of bacteria and fungi were significantly affected by Olsen P, whereas the abundances of archaea were influenced by SOC. Our results suggested crop rotation and manure fertilization (PNON soil) enhanced soil properties and microbial abundance although long-time onion mono-crop (CHON soil) reduced soil fertility. This study can provide information to improve soil quality and sustainability of agro-ecosystems using appropriate agricultural management.

SUPPLEMENTARY INFORMATION

The online version contains supplementary material available at 10.1007/s13205-021-02705-y.

Antimicrobial resistant gene prevalence in soils due to animal manure deposition and long-term pasture management

The persistence of antimicrobial resistant (AMR) genes in the soil-environment is a concern, yet practices that mitigate AMR are poorly understood, especially in grasslands. Animal manures are widely deposited on grasslands, which are the largest agricultural land-use in the United States. These nutrient-rich manures may contain AMR genes. The aim of this study was to enumerate AMR genes in grassland soils following 14-years of poultry litter and cattle manure deposition and evaluate if best management practices (rotationally grazed with a riparian (RBR) area and a fenced riparian buffer strip (RBS), which excluded cattle grazing and poultry litter applications) relative to standard pasture management (continuously grazed (CG) and hayed (H)) minimize the presence and amount of AMR genes. Quantitative PCR (Q-PCR) was performed to enumerate four AMR genes (ermB, sulI, intlI, and bla_ctx-m-32 ) in soil, cattle manure, and poultry litter environments. Six soil samples were additionally subjected to metagenomic sequencing and resistance genes were identified from assembled sequences. Following 14-years of continuous management, ermB, sulI, and intlI genes in soil were greatest (P < 0.05) in samples collected under long-term continuous grazing (relative to conservation best management practices), under suggesting overgrazing and continuous cattle manure deposition may increase AMR gene presence. In general, AMR gene prevalence increased downslope, suggesting potential lateral movement and accumulation based on landscape position. Poultry litter had lower abundance of AMR genes (ermB, sulI, and intlI) relative to cattle manure. Long-term applications of poultry litter increased the abundance of sulI and intlI genes in soil (P < 0.05). Similarly, metagenomic shotgun sequencing revealed a greater total number of AMR genes under long-term CG, while fewer AMR genes were found in H (no cattle manure) and RBS (no animal manure or poultry litter). Results indicate long-term conservation pasture management practices (e.g., RBS and RBR) and select animal manure (poultry litter inputs) may minimize the presence and abundance of AMR genes in grassland soils.

Bacterial community dynamics with rhizosphere of Calotropis procera and Senna alexandrina desert plants in Saudi Arabia

It is of interest to study the rhizobacteria associated with two different desert wild plants, e.g., Calotropis procera and Senna alexandrina compared with bulk soil sample in order to identify signatures of microbes in rhizospheres of the two plants and detect influence of soil microbiome in drawing soil architecture. Analysis of deep sequencing microbial dataset indicated occurrence of 296,642 sequence tags assigned 5,210 OTUs (operational taxonomic units). Species richness in control sample was higher than those of either plant's rhizosphere, while microbial abundance was lower. Principal coordinate analysis (PCoA) plot indicated complete separation of microbiome diversity among groups. Abundances of Pseudomonas stutzeri and Virgibacillus koreensis increased in the rhizosphere of C. procera compared with that of S. alexandrina, while those of Streptococcus sobrinus, Veillonella parvula and unassigned species of Sphingomonas genus increased in rhizosphere of S. alexandrina. Unassigned species of genera Marinobacter, Porticoccus and Alcanivorax only exist in rhizosphere microbiome of C. procera, while unassigned species of genus Pseudomonas only exists in rhizosphere microbiome of Senna alexandrina. High abundances of the two microbes Pseudomonas stutzeri and Virgibacillus koreensis in rhizosphere of C. procera allow the plant to grow well under both normal and saline condition. Also, Marinobacter, Porticoccus and Alcanivorax genera only exist in rhizosphere microbiome of C. procera. These microbes produce siderophores that protect plant from pathogens. Data shows that C. procera might be more protected from microbial pathogens compared with S. alexandrina. The differential abundances or exclusive presence of soil microbes reflect the ability of plant species to survive under biotic and abiotic stresses. Results imply that rhizospheric microbes can be used as biomarkers of plant growth rate and the ability to survive under harsh conditions.

Response of microbial community composition in soils affected by coal mine exploitation

Surface mining activities, despite their benefits, lead to the deterioration of local and regional environmental quality and play a role in global ecosystem pollution. This research aimed to estimate the culturable microbial population structure at five locations near the opencast coal mine "Kakanj" (Bosnia and Herzegovina) via agar plate and phospholipid fatty acids (PLFA) method and to establish its relationship to the physical and chemical properties of soil. Using the ICP-OES method, the heavy metal pollution of all examined locations (overburden, former grass yard, forest, arable soil, and greenhouse) was observed. Substantial variations among the sites regarding the most expressed indicators of heavy metal pollution were noted; Cr, Pb, Ni, and Cu content ranged from 63.17 to 524.47, 20.57 to 349.47, 139.13 to 2785.67, and 25.97 to 458.73 mg/kg, respectively. In the overburden sample, considerable low microbial activity was detected; the bacterial count was approximately 6- to 18-fold lower in comparison with the other samples. PLFA analysis showed the reduction of microbial diversity, reflected through the prevalence of normal and branched saturated fatty acids, their ratio (ranged from 0.92 to 7.13), and the absence of fungal marker 18:2ω6 fatty acid. The principal component analysis showed a strong negative impact of heavy metals Na and B on main microbial and PLFA profiles. In contrast, stock of main chemical parameters, including Ca, K, Fe, and pH, was positively correlated with the microbial community structure.

Divergent gross nitrogen transformation paths in the topsoil and subsoil between abandoned and agricultural cultivation land in irrigated areas

The nitrate concentration in groundwater has increased in many irrigated areas worldwide due to the excessive use of both water and fertilizers. Abandoned farmlands in such irrigated areas may alter the nitrogen (N) cycle because of drastically changed water and N inputs. However, the mechanisms of the N cycle in response to such changes remain unclear. We studied biogeochemical N cycling and microbiological responses from abandoned arable lands (AF), for the topsoil (20 cm depth) and subsoil (100 cm depth) layers, in comparison with irrigation-fertilization (control = CK) land, by using ¹⁵N tracing techniques, the 16S rRNA gene, and real-time PCR (qPCR) to reveal the mechanisms underpinning the N cycle. We found that the biogeochemical environment of abandoned soils shifted their N-cycling pathways. Except for reduced soil moisture, soil properties of total C and N, as well pH, showed improvement in the two layers of AF. But the microbial abundances of ammonia-oxidizing bacteria (AOB-amoA), archaea (AOA-amoA), bacteria and fungi were all significantly lower in the AF; and they presented a consistent trend in the subsoil of the two lands. Significant differences in gross N transformation rates were found for mineralization rates (M_N) and autotrophic nitrification rate (O_NH4) between lands or depths. Compared with AF, M_N was increased by 1.45- and 11.75-times, and O_NH4 by 1.69- and 2.89-times in the topsoil and subsoil of CK, respectively. Our results suggest that the SM × C/N interaction provides insight into the mechanisms underlying the soil microbe-driven changes to transformation rates in nitrogen dynamics after abandoning water-limited lands. The high moisture and N inputs reported here highlight the dynamics and prevalence of M_N and O_NH4, and an increasing the nitrate leaching rate in the unsaturated zone, which poses a major threat to groundwater quality.

Microbial mercury methylation in the cryosphere: Progress and prospects

Mercury (Hg) is one of the most toxic heavy metals, and its cycle is mainly controlled by oxidation-reduction reactions carried out by photochemical or microbial process under suitable conditions. The deposition and accumulation of methylmercury (MeHg) in various ecosystems, including the cryospheric components such as snow, meltwater, glaciers, and ice sheet, and subsequently in the food chain pose serious health concerns for living beings. Unlike the abundance of knowledge about the processes of MeHg production over land and oceans, little is known about the sources and production/degradation rate of MeHg in cryosphere systems. In addition, processes controlling the concentration of Hg and MeHg in the cryosphere remains poorly understood, and filling this scientific gap has been challenging. Therefore, it is essential to study and review the deposition and accumulation by biological, physical, and chemical mechanisms involved in Hg methylation in the cryosphere. This review attempts to address knowledge gaps in understanding processes, especially biotic and abiotic, applicable for Hg methylation in the cryosphere. First, we focus on the variability in Hg concentration and mechanisms of Hg methylation, including physical, chemical, microbial, and biological processes, and transportation in the cryosphere. Then, we elaborate on the mechanism of redox reactions and biotic and abiotic factors controlling Hg methylation and biogeochemistry of Hg in the cryosphere. We also present possible mechanisms of Hg methylation with an emphasis on microbial transformation and molecular function to understand variability in Hg concentration in the cryosphere. Recent advancements in the genetic and physicochemical mechanisms of Hg methylation are also presented. Finally, we summarize and propose a method to study the unsolved issues of Hg methylation in the cryosphere.

Soil bacterial biodiversity is driven by long-term pasture management, poultry litter, and cattle manure inputs

Soil microorganisms are important for maintaining soil health, decomposing organic matter, and recycling nutrients in pasture systems. However, the impact of long-term conservation pasture management on soil microbial communities remains unclear. Therefore, soil microbiome responses to conservation pasture management is an important component of soil health, especially in the largest agricultural land-use in the US. The aim of this study was to identify soil microbiome community differences following 13-years of pasture management (hayed (no cattle), continuously grazed, rotationally grazed with a fenced, un-grazed and unfertilized buffer strip, and a control (no poultry litter or cattle manure inputs)). Since 2004, all pastures (excluding the control) received annual poultry litter at a rate of 5.6 Mg ha^-1. Soil samples were collected at a 0-15 cm depth from 2016-2017 either pre or post poultry litter applications, and bacterial communities were characterized using Illumina 16S rRNA gene amplicon sequencing. Overall, pasture management influenced soil microbial community structure, and effects were different by year (P < 0.05). Soils receiving no poultry litter or cattle manure had the lowest richness (Chao). Continuously grazed systems had greater (P < 0.05) soil community richness, which corresponded with greater soil pH and nutrients. Consequently, continuously grazed systems may increase soil diversity, owing to continuous nutrient-rich manure deposition; however, this management strategy may adversely affect aboveground plant communities and water quality. These results suggest conservation pasture management (e.g., rotationally grazed systems) may not improve microbial diversity, albeit, buffer strips were reduced nutrients and bacterial movement as evident by low diversity and fertility in these areas compared to areas with manure or poultry litter inputs. Overall, animal inputs (litter or manure) increased soil microbiome diversity and may be a mechanism for improved soil health.

Degradation of transgenic Bt-rice straw incorporated with two different paddy soils

Transgenic Bt-rice is rice that has been genetically modified to produce insecticidal proteins (Cry1Ab/Ac) within the plant. Rice straw is incorporated into paddy soils after harvest for fertilization or to improve the soil structure. The incorporation of straw from transgenic Bt-rice may pose risks to the paddy soil system. The decomposition of Bt-rice straw and degradation of Cry1Ab/Ac proteins from the straw were investigated under laboratory conditions. In addition, effects of the incorporation with chopped rice straw on microbial communities in differently textured paddy soils were studied. The results indicated that the incorporation of straw from transgenic Bt-rice might have a slight influence on soil respiration and CH₄ emissions in two paddy soils, i.e. the Silt Loam soil and the Silty Clay soil. Differences were also observed in the cumulative emissions of CO₂ between the two amended paddy soils in addition to the well-known increase in emissions of both CO₂ and CH₄ due to straw incorporation. The Cry1Ab/Ac proteins from straw of transgenic Bt-rice were degraded in paddy soils. The rate of decline in the concentration of Cry1Ab/Ac proteins was different in the two soils. After 29 d of incubation, 61% and 42% of initial Cry1Ab/Ac proteins were detected in the silt loam and silty clay, respectively. As a result of the presence of the rice straw, the abundance of bacteria, archaea, and total cells were increased in two soils. The numbers of bacteria and total cells were 6.4% and 11.5% higher in the silt loam amended with straw of Bt-rice than non-Bt-rice, respectively. The silty clay displayed a similar trend as the silt loam.

Change of soil microbial community under long-term fertilization in a reclaimed sandy agricultural ecosystem

The importance of soil microbial flora in agro-ecosystems is well known, but there is limited understanding of the effects of long-term fertilization on soil microbial community succession in different farming management practices. Here, we report the responses of soil microbial community structure, abundance and activity to chemical (CF) and organic fertilization (OF) treatments in a sandy agricultural system of wheat-maize rotation over a 17-year period. Illumina MiSeq sequencing showed that the microbial community diversity and richness showed no significant changes in bacteria but decreased in fungi under both CF and OF treatments. The dominant species showing significant differences between fertilization regimes were Actinobacteria, Acidobacteria and Ascomycota at the phylum level, as well as some unclassified genera of other phyla at the genus level. As expected, soil organic matter content, nutrient element concentrations and bacterial abundance were enhanced by both types of fertilization, especially in OF, but fungal abundance was inhibited by OF. Redundancy analysis revealed that soil enzyme activities were closely related to both bacterial and fungal communities, and the soil nutrient, texture and pH value together determined the community structures. Bacterial abundance might be the primary driver of crop yield, and soil enzyme activities may reflect crop yield. Our results suggest a relatively permanent response of soil microbial communities to the long-term fertilization regimes in a reclaimed sandy agro-ecosystem from a mobile dune, and indicate that the appropriate dosage of chemical fertilizers is beneficial to sandy soil sustainability.

Influence of biochars on the accessibility of organochlorine pesticides and microbial community in contaminated soils

Biochar can be used as a promising potential substance to reduce the availability of toxic elements and compounds in contaminated soils but its effects on the accessibility of pesticides and microbiological interactions still remain unclear. Here, 65 day incubation experiments were conducted to investigate the efficacy of biochars on the accessibility of 21 different organochlorine pesticides (OCPs), and also to evaluate their influence on soil microbial community. The tested soil was collected from an agricultural field, containing loamy sand texture, and historically contaminated with high concentrations of OCPs. The soil was amended with four different kinds of biochars: sewage sludge biochar (SSBC), peanut shells biochar (PNBC), rice straw biochar (RSBC), and soybean straw biochar (SBBC). The results indicated that biochar-amendments had strong effects upon OCP accessibility over time and can act as super sorbent. Despite greater persistence of OCPs in soil, the application of selected biochars significantly (p < 0.01) reduced the accessibility of ∑OCPs in the amended soil in the order of SSBC (8-69%), PNBC (11-75%), RSBC (6-67%), and SBBC (14-86%), as compared to the control soil during 0-65 d incubation period. Moreover, the findings from total phospholipid acid (PLFA) and Illumina next-generation sequencing revealed that the incorporation of biochar have altered the soil microbial community structure over time. Higher abundances of Proteobacteria, firmicutes, Gemmatimonadetes, and Actinobacteria were found in biochar amendments. However, the relative abundances of Acidobacteria and Chloroflexi decreased, following biochar addition. The findings of these experiments suggest that biochar addition to soil at the rate of 3% (w/w) could be advantageous for decreasing accessibility of OCPs, enhancing the soil microbial communities, and their subsequent risk to environment and food chain contamination.

Impact of ampicillin on the nitrogen removal, microbial community and enzymatic activity of activated sludge

The performance, nitrogen removal rate, extracellular polymeric substances (EPS), microbial community and enzymatic activity of activated sludge have been assessed in a sequencing batch reactor under ampicillin stress. The chemical oxygen demand and ammonia removal kept relatively stable at 0-30 mg/L ampicillin. No obvious nitrite and nitrate accumulation was found in the effluent. However, the oxygen utilization rate, nitrification rate and denitrification rate declined with the increment of ampicillin concentration. The activities of dehydrogenase and microbial enzymes relating to nitrogen removal were inhibited under ampicillin stress. Ampicillin at 20 and 30 mg/L heightened the microbial lactate dehydrogenase release and reactive oxygen species production. Ampicillin promoted the production of EPS, loosely bound EPS and tightly bound EPS and affected their chemical composition. Additionally, the protein/polysaccharide ratios in the EPS and the sludge settleability reduced with the increment of ampicillin concentration. Ampicillin obviously affected the relative abundance of nitrifying- and denitrifying bacteria.

Effects of the herbicide mesotrione on soil enzyme activity and microbial communities

Mesotrione (2-[4-(methylsulfonyl)-2-nithobenzoyl]-1, 3-cyclohexanedione) is a selective triketone herbicide that has been widely used in corn production for the past 15 years. However, its potential for risk to soil ecosystems is poorly documented. The present study investigated the soil enzyme activity and soil microbial community responses to a 20 days' mesotrione exposure at doses of 0.1, 1.0 and 5.0 mg/kg. On days 2, 5, 10 and 20, activities of soil β-glucosidase, urease and acid phosphatase, soil microbe abundances, soil microbial community structure and abundance of the AOA-amoA and AOB-amoA genes were measured. Results showed that activities of urease and acid phosphatase were relatively stable, with no difference found between the mesotrione-treated group and control at the end of exposure. But β-glucosidase activity was reduced in the 5.0 mg/kg mesotrione treatment. In the 1.0 and 5.0 mg/kg mesotrione-treated soil, abundance of bacteria, fungi and actinomycetes all were reduced. In the 0.1 mg/kg mesotrione-treated soil, only fungi abundance was reduced by the end of the exposure. The analysis of terminal restriction fragment length polymorphism (T-RFLP) revealed soil microbial community structure could be affected by mesotrione at all experimental doses, and microbial diversity declined slightly after mesotrione exposure. Abundance of AOA-amoA and AOB-amoA genes were reduced markedly in 1.0 and 5.0 mg/kg mesotrione-treated soil. The present study suggests that mesotrione at higher doses might induce negative impacts on soil microbes, a finding which merits additional research and which should be accounted for when application of this herbicide is considered.

Color characterization of anammox granular sludge: Chromogenic substance, microbial succession and state indication

Vision is a direct and convenient way to get information, and color characteristics are important visual information to identify objects. In this study, the L*a*b* color space was introduced for the first time to digitize the surface color of anammox granular sludge (AnGS). Three AnGSs under typical biological loading rates were chosen and the color value a*/b* was found to have a positive correlation with the specific anammox activity and the biological loading rate of AnGS. Cytochrome c was detected to be the key chromogenic substance determining the red hue of AnGS. The concentration of cytochrome c was highly consistent with the abundance of anammox bacteria. Nitrospira was observed to compete with Candidatus Kuenenia for nitrite under survival state, resulting in the obvious decrease of a* value; while the growth of sulfur-related Limnobacter and Thiobacillus was enhanced under starvation state, leading to the production of Fe-S compounds covering over the surface and decrease of a* and b* value simultaneously. The unique color characteristics of AnGS were evaluated as a visual indicator to serve the on-line control and better judgement of anammox process.

Influence of Macrofaunal Burrows on Extracellular Enzyme Activity and Microbial Abundance in Subtropical Mangrove Sediment

Bioturbation and bioirrigation induced by burrowing macrofauna are recognized as important processes in aquatic sediment since macrofaunal activities lead to the alteration of sediment characteristics. However, there is a lack of information on how macrofauna influence microbial abundance and extracellular enzyme activity in mangrove sediment. In this study, the environmental parameters, extracellular enzyme activities, and microbial abundance were determined and their relationships were explored. Sediment samples were taken from the surface (S) and lower layer (L) without burrow, as well as crab burrow wall (W) and bottom of crab burrow (B) located at the Mai Po Nature Reserve, Hong Kong. The results showed that the burrowing crabs could enhance the activities of oxidase and hydrolases. The highest activities of phenol oxidase and acid phosphatase were generally observed in B sediment, while the highest activity of N-acetyl-glucosaminidase was found in W sediment. The enzymatic stoichiometry indicated that the crab-affected sediment had similar microbial nitrogen (N) and phosphorous (P) availability relative to carbon (C), lower than S but higher than L sediment. Furthermore, it was found that the highest abundance of both bacteria and fungi was shown in S sediment, and B sediment presented the lowest abundance. Moreover, the concentrations of phosphorus and soluble phenolics in crab-affected sediment were almost higher than the non-affected sediment. The alterations of phenolics, C/P and N/P ratios as well as undetermined environmental factors by the activities of crabs might be the main reasons for the changes of enzyme activity and microbial abundance. Finally, due to the important role of phenol oxidase and hydrolases in sediment organic matter (SOM) decomposition, it is necessary to take macrofaunal activities into consideration when estimating the C budget in mangrove ecosystem in the future.

Bioaugmentation and rhizosphere-assisted biodegradation as strategies for optimization of the dissipation capacity of biobeds

Biobeds are on-farm biodepuration systems whose efficiency rely on their high pesticide biodegradation capacity. We evaluated two optimization strategies, bioaugmentation and/or rhizosphere-assisted biodegradation, to maximize the dissipation capacity of biobeds. Iprodione was used as a model pesticide. Its dissipation and metabolism was determined in a biobed packing material inoculated with an iprodione-degrading Arthrobacter strain C1 (bioaugmentation, treatments B+C1) and/or seeded with ryegrass (rhizosphere-assisted biodegradation, treatments B+P). The impact of those strategies on the activity and composition of the microbial community was determined. Bioaugmentation accelerated the dissipation of iprodione which was further enhanced in the bioaugmented, rhizosphere-assisted treatment (treatment B+P+C1, Half-life (DT₅₀) = 3.4 d), compared to the non-bioaugmented, non rhizosphere-assisted control (DT₅₀ = 9.5 d, treatment B). Bioaugmentation resulted in the earlier formation of intermediate formation of metabolites I (3,5-dichlorophenyl-carboxamide), II (3,5-dichlorophenylurea acetate) and 3,5-dichloroaniline (3,5-DCA). The latter was further dissipated by the indigenous microbial community. Acid phosphatase (AP) and β-glucosidase (GLU) were temporarily stimulated in rhizosphere-assisted treatments, whereas a stimulation of the fluorescein diacetate (FDA) hydrolytic activity in the bioaugmented treatments coincided with the hydrolysis of iprodione. q-PCR showed that changes in the abundance of alpha-proteobacteria and firmicutes was driven by the presence of rhizosphere while bioaugmentation had no significant effect.

Plant community influence on soil microbial response after a wildfire in Sierra Nevada National Park (Spain)

Plant community influence on microbial response after fire has been studied in a Sierra Nevada National Park area affected by a wildfire in 2005. Two different plant communities adapted to different altitudes were selected to analyse possible differences on soil microbial recolonisation process after fire, in oak forest and high mountain shrub communities. Microbial abundance, activity and community composition were monitored to evaluate medium-term changes. Microbial abundance was studied by mean of microbial biomass carbon and plate count methods; microbial activity was analysed by microbial respiration and bacterial growth while microbial community composition was determined by analysing phospholipid fatty acid pattern. Under unburnt conditions oak forest showed higher nutrient content, pH and microbial abundance and activity values than the high mountain shrubs community. Different parameters studied showed different trends with time, highlighting important changes in microbial community composition in high mountain shrubs from first sampling to the second one. Post-fire recolonisation process was different depending on plant community studied. Highlighting fungal response and microbial activity were stimulated in burnt high mountain shrubs community whilst it was negatively affected in oak forest. Fire induced changes in oak forest were almost neutralized 20months after the fire, while high mountain shrubs community still showed fire-induced changes at the end of the study.

Alteration of extracellular enzyme activity and microbial abundance by biochar addition: Implication for carbon sequestration in subtropical mangrove sediment

Biochar has attracted more and more attention due to its essential role in adsorbing pollutants, improving soil fertility, and modifying greenhouse gas emission. However, the influences of biochar on extracellular enzyme activity and microbial abundance are still lack and debatable. Currently, there is no information about the impact of biochar on the function of mangrove ecosystems. Therefore, we explored the effects of biochar on extracellular enzyme activity and microbial abundance in subtropical mangrove sediment, and further estimated the contribution of biochar to C sequestration. In this study, sediments were amended with 0 (control), 0.5, 1.0 and 2.0% of biochar and incubated at 25 °C for 90 days. After incubation, enzyme activities, microbial abundance and the increased percentage of sediment organic C content were determined. Both increase (phenol oxidase and β-glucosidase) and decrease (peroxidase, N-acetyl-glucosaminidase and acid phosphatase) of enzyme activities were observed in biochar treatments, but only peroxidase activity showed statistical significance (at least p < 0.01) compared to the control. Moreover, the activities of all enzymes tested were significantly related to the content of biochar addition (at least p < 0.05). On the other hand, bacterial and fungal abundance in biochar treatments were remarkably lower than control (p < 0.001), and the significantly negative relationship (p < 0.05) between bacterial abundance and the content of biochar was found. Additionally, the increased percentage of organic C gradually increased with biochar addition rate, which provided evidence for applying biochar to mitigate climate change. Given the importance of microorganisms and enzyme activities in sediment organic matter decomposition, the increased C sequestration might be explained by the large decrease of microbial abundance and enzyme activity after biochar intervention.

Microbial Community and Greenhouse Gas Fluxes from Abandoned Rice Paddies with Different Vegetation

The area of rice paddy fields has declined continuously in East Asian countries due to abandonment of agriculture and concurrent socioeconomic changes. When they are abandoned, rice paddy fields generally transform into wetlands by natural succession. While previous studies have mainly focused on vegetation shifts in abandoned rice paddies, little information is available about how these changes may affect their contribution to wetland functions. As newly abandoned fields proceed through succession, their hydrology and plant communities often change. Moreover, the relationships between these changes, soil microbial characteristics, and emissions of greenhouse gasses are poorly understood. In this study, we examined changes over the course of secondary succession of abandoned rice paddies to wetlands and investigated their ecological functions through changes in greenhouse gas fluxes and microbial characteristics. We collected gas and soil samples in summer and winter from areas dominated by Cyperaceae, Phragmites, and Sphagnum in each site. We found that CO2 emissions in summer were significantly higher than those in winter, but CH4 and N2O emission fluxes were consistently at very low levels and were similar among seasons and locations, due to their low nutrient conditions. These results suggest that microbial activity and abundance increased in summer. Greenhouse gas flux, soil properties, and microbial abundance were not affected by plant species, although the microbial community composition was changed by plant species. This information adds to our basic understanding of the contribution of wetlands that are transformed from abandoned rice paddy systems.

Effects of pH on nitrogen transformations in media-based aquaponics

To investigate the effects of pH on performance and nitrogen transformations in aquaponics, media-based aquaponics operated at pH 6.0, 7.5 and 9.0 were systematically examined and compared in this study. Results showed that nitrogen utilization efficiency (NUE) reached its maximum of 50.9% at pH 6.0, followed by 47.3% at pH 7.5 and 44.7% at pH 9.0. Concentrations of nitrogen compounds (i.e., TAN, NO2(-)-N and NO3(-)-N) in three pH systems were all under tolerable levels. pH had significant effect on N2O emission and N2O conversion ratio decreased from 2.0% to 0.6% when pH increased from 6.0 to 9.0, mainly because acid environment would inhibit denitrifiers and lead to higher N2O emission. 75.2-78.5% of N2O emission from aquaponics was attributed to denitrification. In general, aquaponics was suggested to maintain pH at 6.0 for high NUE, and further investigations on N2O mitigation strategy are needed.

Microbial abundance and community in subsurface flow constructed wetland microcosms: role of plant presence

In this research, the role of plants in improving microorganism growth conditions in subsurface flow constructed wetland (CW) microcosms was determined. In particular, microbial abundance and community were investigated during summer and winter in Phragmites australis-planted CW microcosms (PA) and unplanted CW microcosms (control, CT). Results revealed that the removal efficiencies of pollutants and microbial community structure varied in winter with variable microbial abundance. During summer, PA comprised more dominant phyla (e.g., Proteobacteria, Actinobacteria, and Bacteroidetes), whereas CT contained more Cyanobacteria and photosynthetic bacteria. During winter, the abundance of Proteobacteria was >40 % in PA but dramatically decreased in CT. Moreover, Cyanobacteria and photosynthetic bacterial dominance in CT decreased. In both seasons, bacteria were more abundant in root surfaces than in sand. Plant presence positively affected microbial abundance and community. The potential removal ability of CT, in which Cyanobacteria and photosynthetic bacteria were abundant during summer, was more significantly affected by temperature reduction than that of PA with plant presence.

Composition, taxonomy and functional diversity of the oropharynx microbiome in individuals with schizophrenia and controls

The role of the human microbiome in schizophrenia remains largely unexplored. The microbiome has been shown to alter brain development and modulate behavior and cognition in animals through gut-brain connections, and research in humans suggests that it may be a modulating factor in many disorders. This study reports findings from a shotgun metagenomic analysis of the oropharyngeal microbiome in 16 individuals with schizophrenia and 16 controls. High-level differences were evident at both the phylum and genus levels, with Proteobacteria, Firmicutes, Bacteroidetes, and Actinobacteria dominating both schizophrenia patients and controls, and Ascomycota being more abundant in schizophrenia patients than controls. Controls were richer in species but less even in their distributions, i.e., dominated by fewer species, as opposed to schizophrenia patients. Lactic acid bacteria were relatively more abundant in schizophrenia, including species of Lactobacilli and Bifidobacterium, which have been shown to modulate chronic inflammation. We also found Eubacterium halii, a lactate-utilizing species. Functionally, the microbiome of schizophrenia patients was characterized by an increased number of metabolic pathways related to metabolite transport systems including siderophores, glutamate, and vitamin B12. In contrast, carbohydrate and lipid pathways and energy metabolism were abundant in controls. These findings suggest that the oropharyngeal microbiome in individuals with schizophrenia is significantly different compared to controls, and that particular microbial species and metabolic pathways differentiate both groups. Confirmation of these findings in larger and more diverse samples, e.g., gut microbiome, will contribute to elucidating potential links between schizophrenia and the human microbiota.