Microbial community structure and functional genes drive soil priming effect following afforestation

Afforestation substantially modifies native soil organic carbon (SOC) decomposition via plant carbon inputs (the priming effect), and in turn, triggers vital biogeochemical processes that influence the regulation of soil carbon dynamics. Soil microbes are crucial in regulating the direction and magnitude of the priming effect. In the present study, we performed metagenomic sequencing and ¹³C-glucose labeling analyses of microbial communities and priming effects across a Robinia pseudoacacia afforestation chronosequence (14-, 20-, 30-, and 45-year-old stands) in the Loess Plateau in China, with adjacent farmland being selected as a control. Our results revealed that the cumulative priming effect across five sites along the afforestation chronosequence initially increased and approached a peak value in the 20-year-old stand, after which it declined. The priming effect was predominantly driven by the microbial community structure (i.e., the fungal-to-bacterial ratios and relative abundances of Proteobacteria and Actinobacteria), and stable C decomposition genes and C-degrading enzymes. Specifically, among the key functional genes correlated with priming effect, which were identified in orders Rhizobiales and Pseudonocardiales, considerably promoted SOC priming. Overall, our findings indicate that afforestation alters soil microbial community structure and function, particularly with respect to enhancing stable soil C decomposition genes, which may promote SOC priming. The findings of the present study could enhance our understanding of fresh C input-induced changes associated with C mineralization in the context of the revegetation of ecologically fragile areas.

The effect of phosphate mining activities on rhizosphere bacterial communities of surrounding vegetables and crops

The effects of phosphate mining on rhizosphere bacteria in surrounding vegetables and crops, including Lactuca sativa, Glycine max, and Triticum aestivum, are assessed in this study. As results, phosphate mining significantly increased the contents of some large elements, trace elements, and heavy metals in the surrounding agricultural soil, including phosphorus, magnesium, boron, cadmium, lead, arsenic, zinc, and chromium (P < 0.05). The community richness and diversity of bacteria in rhizosphere of the three crops were significantly reduced by phosphate mining (P < 0.05). Abundances of Sphingomonas and RB41 in the rhizosphere soil of phosphate mining area improved compared with the baseline in the non-phosphate mining area. Beta diversity analysis indicated that phosphate mining led to the differentiation of bacterial community structure in plant rhizospheres. Bacterial metabolic analysis indicated that different plant rhizosphere microbial flora developed various metabolic strategies in response to phosphate mining stress, including enriching unsaturated fatty acids, antibiological transport systems, cold shock proteins, etc. This study reveals the interaction between crops, rhizosphere bacteria, and soil pollutants. Select differentiated microbial strains suitable for specific plant rhizosphere environments are necessary for agricultural soil remediation. Additionally, the problem of destruction of agricultural soil and microecology caused by phosphate mining must be solved.

Metagenomic analysis reveals the different characteristics of microbial communities inside and outside the karst tiankeng

Background

Karst tiankengs serve as a reservoir of biodiversity in the degraded karst landscape areas. However, the microbial diversity of karst tiankengs is poorly understood. Here, we investigated the composition and function of the microbial community in a karst tiankeng.

Results

We found that habitat differences inside and outside the karst tiankeng changed the composition and structure of the soil microbial communities, and the dominant phyla were Proteobacteria, Actinobacteria, Chloroflexi and Acidobacteria. The Shannon–Wiener diversity of microbial communities inside and outside the tiankeng was significantly different, and it was higher inside the tiankeng (IT). Venn and LEfSe analysis found that the soil microbial communities inside the tiankeng had 640 more endemic species and 39 more biomarker microbial clades than those identified outside of the tiankeng (OT)..Functional prediction indicated that soil microorganisms in outside the tiankeng had a high potential for carbohydrate metabolism, translation and amino acid metabolism. There were biomarker pathways associated with several of human diseases at both IT and OT sites. Except for auxiliary activities (AA), other CAZy classes had higher abundance at IT sites, which can readily convert litter and fix carbon and nitrogen, thereby supporting the development of underground forests. The differences in microbial communities were mainly related to the soil water content and soil total nitrogen.

Conclusions

Our results provide a metagenomic overview of the karst tiankeng system and provide new insights into habitat conservation and biodiversity restoration in the area.

Supplementary Information

The online version contains supplementary material available at 10.1186/s12866-022-02513-1.

Impact of hexachlorocyclohexane addition on the composition and potential functions of the bacterial community in red and purple paddy soil

Soil studies have reported the effect of Hexachlorocyclohexane (HCH) on soil microbial communities. However, how soil microbial communities and function shift after HCH addition into the red and purple soil remains unclear. Here, we analyzed the HCH residue fate, and the functional composition and structure of microbial communities to HCH in the two soils. Under the 100 g/ha and 1000 g/ha treatment, the dissipation rate of HCH was 0.0386 and 0.0273 in the purple soil, 0.0145 and 0.0195 in the red soil. The enrichment of HCH degrading genes leads to a higher HCH dissipation rate in the purple soil. PCoA results demonstrated that HCH addition has a different effect on the community diversity in the two soils, and Proteobacteria and Acidobacteria were the major phyla in the two soils. The soil microbiome average variation degree values of red soil were higher than purple soil, which indicated that the soil microbiome in the purple soil was more stable than in the red soil under HCH addition. PICRUSt2 results indicated that functional genes involved in the carbon, nitrogen biogeochemical cycles and HCH degradation were more tolerant to HCH addition in the purple soil. This study provides new insights into understanding of the effect of HCH addition on soil microbial communities and function in the red and purple paddy soil.

New insights into the role of molecular structures on the fate and behavior of antibiotics in an osmotic membrane bioreactor

Osmotic membrane bioreactors (OMBRs) have been applied to enhance removal of antibiotics, however, information on the effects of molecular structures on the behavior of antibiotics is still lacking. Herein, adsorption kinetics, transformation pathways, and membrane rejection mechanisms of OMBRs were investigated by adding two typical antibiotics (i.e., sulfadiazine, SDZ, and tetracycline hydrochloride, TC-HCl). 80.70-91.12% of TC-HCl was removed by adsorption and biodegradation, while 17.50-75.14% of SDZ was removed by membrane rejection; this depended on its concentration due to reduced electrostatic interactions and hydrophobic adsorption. The adsorption capacity of TC-HCl (i.e., 1.34±0.01 mg/g) was significantly higher than that of SDZ (i.e., 0.18±0.03 mg/g) due to enhanced π-π interactions, hydrogen bonding and improved electrostatic interactions. The abundant production of polysaccharide-like substances from TC-HCl biodegradation contributed to microbial metabolism and thus enhanced microbial function during TC-HCl biotransformation. The primary degradation pathways were determined by microbial function analysis, and the primary intermediates from TC-HCl degradation were less toxic than those from SDZ degradation due to the different reactions of amino groups. These results and the corresponding mechanism provide a theoretical foundation for the further development of OMBR technology for highly efficient treatment of antibiotic wastewater.

Microbial adaptation and response to high ammonia concentrations and precipitates during anaerobic digestion under psychrophilic and mesophilic conditions

This study explored microbial adaptation to high ammonia concentrations (<1000 mg/L to 4000 mg/L) during anaerobic digestion (AD) under psychrophilic and mesophilic conditions, the latter of which yielded precipitates facilitating investigation of microbial response. The experimental setup was performed at bench-scale using microbial consortia from four different operating anaerobic digesters treating different organic wastes (WW-wastewater sludge, MN-manure, FW- food waste and CO-co-digestion (FW & MN)). Adaptation experiments were conducted with semi-continuous flow mode to resemble large-scale operation. Metagenome and 16S RNA analysis were performed for the first time in a psychrophilic reactor during an ammonia acclimation process. These analyses were also performed in mesophilic reactor exposed to precipitates and high ammonia levels. Diversity reduced when adaptation occurred successfully from 1.1 to 4 g/L of total ammonia nitrogen (TAN) under psychrophilic conditions, while the microbial community became more diverse under mesophilic conditions with ammonia inhibition. We report for the first time Methanocorposculum as a robust hydrogenotrophic methanogen at high ammoniacal concentrations under psychrophilic conditions. Additionally, Methanosarcina was present in low and high ammoniacal concentrations in mesophilic conditions, but there was a shift in species dominance. Methanosarcina barkeri stands out as a more resilient methanogen compared to Methanosarcina mazei, which initially dominated at <1.1 g/L TAN. We also explored the effects of sudden precipitates on methanogenic communities and methane production when they occurred under mesophilic conditions in two reactors. Methane production declined by more than 50% when precipitates occurred and was accompanied by pH reduction and VFA accumulation. Diversity data corroborated that methanogens were severely reduced. These two reactors were not able to recover with 50 days of added operation, demonstrating potential for long-term negative impacts of precipitate formation on AD performance stemming from negative impact to methanogenic communities.

New insights into restoring microbial communities by side-stream supersaturated oxygenation to improve the resilience of rivers affected by combined sewer overflows

Combined sewer overflows (CSOs) are a dominant contributor to urban river pollution. Therefore, reducing the environmental impacts of CSOs and improving the self-purification capacity of water bodies are essential. In this study, the side-stream supersaturation (SSS) oxygenation was applied to restore microbial function of rivers which are affected by CSOs to improve the self-purification capacity. The results showed that apart from the dissolved organic matter inputs from CSO event, the sediment had become an important contributor to pollution in the studied river. After the long-term (46 d) implementation of SSS oxygenation, dissolved oxygen and the oxidation-reduction potential of the river water increased by 98% and 238%, respectively, compared to emergency control measures implemented following individual CSO events. The NH₃-N concentrations and the chemical oxygen demand also decreased by 20% and 45%, respectively. In addition, the occurrence of microbial functions related to information storage and processing, and cellular process and signaling, increased by 1.87% and 0.82% in response to SSS oxygenation, respectively, and the Shannon index of the sediment microbial community increased by more than 15%. The frequencies of genes related to nitrification and sulfur oxidation also increased by 20-450% and >50%, respectively. This research provides new insights into the ecological restoration of rivers affected by CSOs.

Tree cover mediate indices related to the content of organic matter and the size of microbial population in semi-arid ecosystems

The type of vegetation cover affects the contents of organic matter and other soil features that can lead to variability of soil microbial processes, which play a key role in the nutrient cycle. This issue is especially important in mountainous semi-arid ecosystems, which have been introduced as fragile and vulnerable habitats. In the present study, labile contents of soil organic matter (SOM), microbial and enzymatic indices under the influence of forest and rangeland cover [i.e. natural forest with dominant species of Zelkova carpinifolia (Pall.) K. Koch. And three rangeland covers, converted form forest site almost 30 years ago, with dominant species of Festuca ovina L. Dactylis glomerata L. and Stachys byzantina K. Koch.] in Northern Iran have been considered including seasonal changes. The study aimed to investigate i) the effect of forest conversion to rangelands on SOM fractions, (ii) temporal dynamics of soil microbial processes and enzyme functions in different vegetation types, and (iii) determining the relationship between indices related to the content of organic matter and the size of microbial population in mountain ecosystems. Results showed that Zelkova tree type enhanced the levels of SOM contents, carbon and nutrient (nitrogen, phosphorous, potassium, calcium and magnesium) pools, and also with higher values in the summer season, the size of microbial population and processes. Additionally, the SOM turnover and microbial efficiency were almost suppressed in order to Zelkova > Festuca > Dactylis > Stachys vegetation types, respectively. Based on the obtained results, it can be concluded that the presence of tree cover in mountain ecosystems can strengthen soil function and create fertile islands. Therefore, the protection of natural forests is emphasized for the proper management and sustainability of habitats in semi-arid regions.

Soil redox dynamics under dynamic hydrologic regimes - A review

Electron transfer (redox) reactions, mediated by soil microbiota, modulate elemental cycling and, in part, establish the redox poise of soil systems. Understanding soil redox processes significantly improves our ability to characterize coupled biogeochemical cycling in soils and aids in soil health management. Redox-sensitive species exhibit different reactivity, mobility, and toxicity subjected to their redox state. Thus, it is crucial to quantify the redox potential (E_h) in soils and to characterize the dominant redox couples therein. Several, often coupled, external drivers, can influence E_h. Among these factors, soil hydrology dominates. It controls soil physical properties that in turn further regulates E_h. Soil spatial heterogeneity and temporally dynamic hydrologic regimes yield complex distributions of E_h. Soil redox processes have been studied under various environmental conditions, including relatively static and dynamic hydrologic regimes. Our focus here is on dynamic, variably water-saturated environments. Herein, we review previous studies on soil redox dynamics, with a specific focus on dynamic hydrologic regimes, provide recommendations on knowledge gaps, and targeted future research needs and directions. We review (1) the role of soil redox conditions on the soil chemical-species cycling of organic carbon, nitrogen, phosphorus, redox-active metals, and organic contaminants; (2) interactions between microbial activity and redox state in the near-surface and deep subsurface soil, and biomolecular methods to reveal the role of microbes in the redox processes; (3) the effects of dynamic hydrologic regimes on chemical-species cycling and microbial dynamics; (4) the experimental setups for mimicking different hydrologic regimes at both laboratory and field scales. Finally, we identify the current knowledge gaps related to the study of soil redox dynamics under different hydrologic regimes: (1) fluctuating conditions in the deep subsurface; (2) the use of biomolecular tools to understand soil biogeochemical processes beyond nitrogen; (3) limited current field measurements and potential alternative experimental setups.

Polycyclic aromatic hydrocarbon and n-alkane pollution characteristics and structural and functional perturbations to the microbial community: a case-study of historically petroleum-contaminated soil

Characterization of the typical petroleum pollutants, polycyclic aromatic hydrocarbons (PAHs) and n-alkanes, and indigenous microbial community structure and function in historically contaminated soil at petrol stations is critical. Five soil samples were collected from a petrol station in Beijing, China. The concentrations of 16 PAHs and 31 n-alkanes were measured by gas chromatography-mass spectrometry. The total concentrations of PAHs and n-alkanes ranged from 973 ± 55 to 2667 ± 183 μg/kg and 6.40 ± 0.38 to 8.65 ± 0.59 mg/kg (dry weight), respectively, which increased with depth. According to the observed molecular indices, PAHs and n-alkanes originated mostly from petroleum-related sources. The levels of ΣPAHs and the total toxic benzo[a]pyrene equivalent (ranging from 6.41 to 72.54 μg/kg) might exert adverse biological effects. Shotgun metagenomic sequencing was employed to investigate the indigenous microbial community structure and function. The results revealed that Proteobacteria and Actinobacteria were the most abundant phyla, and Nocardioides and Microbacterium were the important genera. Based on COG and KEGG annotations, the highly abundant functional classes were identified, and these functions were involved in allowing microorganisms to adapt to the pressure from contaminants. Five petroleum hydrocarbon degradation-related genes were annotated, revealing the distribution of degrading microorganisms. This work facilitates the understanding of the composition, source, and potential ecological impacts of residual PAHs and n-alkanes in historically contaminated soil.

Characterization of the rumen microbiota and its relationship with residual feed intake in sheep

Feed efficiency is a highly important economic trait in sheep production and has a significant impact on the economic benefits of sheep farming. Microbial fermentation of the rumen has a vital role in the host's nutrition; the rumen microbiota might affect host feed efficiency. However, the relationship between the rumen microbiota and feed efficiency in sheep is unclear. In the present study, the microbiota of 195 Hu sheep was investigated and their residual feed intake (RFI), a commonly used measure of feed efficiency, was determined. From birth, all sheep were subjected to the same management practices. At slaughter, samples of liquid rumen contents were collected and subjected to amplicon sequencing for the 16S rDNA gene on the IonS5™XL platform. To identify the bacterial taxa differentially represented at the genus or higher taxonomy levels, we used linear discriminant analysis coupled with effect size and curve fitting. In the sheep rumen, the four most abundant phyla were Firmicutes, Bacteroidetes, Fibrobacteres, and Proteobacteria; and the dominant genera were unidentified Prevotellaceae, Fibrobacter, unidentified Lachnospiraceae, Saccharofermentans, and Succinivibrio. Pathway analysis of the 16S rDNA sequencing data from the rumen microbiota identified that carbohydrate metabolism was enriched. Using α-diversity analysis, we further identified that Observed species, ACE, Good's coverage, and Chao1 are more abundant (P < 0.01) in the low-RFI (L-RFI) group compared to the high-RFI (H-RFI) group. High-RFI sheep had a higher abundance of three bacterial taxa (Prevotellaceae, Negativicutes, and Selenomonadales), and one taxa was overrepresented in the L-RFI sheep (Succinivibrio), respectively. Furthermore, model fitting showed that Veillonellaceae, Sphaerochaeta, Negativibacillus, Saccharofermentans, and members of the Tenericutes, Kiritimatiellaeota, Deltaproteobacteria, and Campylobacterales were correlated with the sheep RFI classification and thus were indicative of a role in animal efficiency. Tax4Fun analysis revealed that metabolic pathways such as "energy metabolism," "metabolism of cofactors and vitamins," "poorly characterized," and "replication recombination and repair proteins" were enriched in the rumen from H-RFI sheep, and "genetic information processing" and "lipopolysaccharide biosynthesis" were overrepresented in L-RFI sheep rumen. In addition, six Kyoto Encyclopedia of Genes and Genomes orthology pathways were identified as different between H-RFI and L-RFI groups. In conclusion, the low RFI phenotype (efficient animals) consistently (or characteristically) exhibited a more abundant and diverse microbiome in sheep.

An integrated insight into bioleaching performance of chalcopyrite mediated by microbial factors: Functional types and biodiversity

Six artificial communities with different function or biodiversity were reconstructed by six typical bioleaching species for chalcopyrite leaching. Absence of sulfur oxidizers in communities significantly reduced copper extraction rates, and low diversity communities also exhibited slightly poor bioleaching performances. The variations of pH, redox potential, ferrous and copper ions indicated that the community with both sulfur oxidizers and high diversity showed fast adaptation to the environment and rapid dissolution of chalcopyrite. Integrated analysis of mineralogical and microbial parameters demonstrated that functional types of microorganisms made more contributions in mediating chalcopyrite dissolution than microbial diversity. Further correlation analysis between microbial types and chalcopyrite dissolution performances showed that sulfur oxidizers, especially Acidithiobacillus caldus, could greatly accelerate chalcopyrite dissolution by regulating solution physicochemical factors, such as redox potential and pH. This study provided a theoretical basis for improving bioleaching efficiency by balancing microbial functional types and biodiversity.

Microbial function and genital inflammation in young South African women at high risk of HIV infection

BACKGROUND

Female genital tract (FGT) inflammation is an important risk factor for HIV acquisition. The FGT microbiome is closely associated with inflammatory profile; however, the relative importance of microbial activities has not been established. Since proteins are key elements representing actual microbial functions, this study utilized metaproteomics to evaluate the relationship between FGT microbial function and inflammation in 113 young and adolescent South African women at high risk of HIV infection. Women were grouped as having low, medium, or high FGT inflammation by K-means clustering according to pro-inflammatory cytokine concentrations.

RESULTS

A total of 3186 microbial and human proteins were identified in lateral vaginal wall swabs using liquid chromatography-tandem mass spectrometry, while 94 microbial taxa were included in the taxonomic analysis. Both metaproteomics and 16S rRNA gene sequencing analyses showed increased non-optimal bacteria and decreased lactobacilli in women with FGT inflammatory profiles. However, differences in the predicted relative abundance of most bacteria were observed between 16S rRNA gene sequencing and metaproteomics analyses. Bacterial protein functional annotations (gene ontology) predicted inflammatory cytokine profiles more accurately than bacterial relative abundance determined by 16S rRNA gene sequence analysis, as well as functional predictions based on 16S rRNA gene sequence data (p < 0.0001). The majority of microbial biological processes were underrepresented in women with high inflammation compared to those with low inflammation, including a Lactobacillus-associated signature of reduced cell wall organization and peptidoglycan biosynthesis. This signature remained associated with high FGT inflammation in a subset of 74 women 9 weeks later, was upheld after adjusting for Lactobacillus relative abundance, and was associated with in vitro inflammatory cytokine responses to Lactobacillus isolates from the same women. Reduced cell wall organization and peptidoglycan biosynthesis were also associated with high FGT inflammation in an independent sample of ten women.

CONCLUSIONS

Both the presence of specific microbial taxa in the FGT and their properties and activities are critical determinants of FGT inflammation. Our findings support those of previous studies suggesting that peptidoglycan is directly immunosuppressive, and identify a possible avenue for biotherapeutic development to reduce inflammation in the FGT. To facilitate further investigations of microbial activities, we have developed the FGT-DB application that is available at http://fgtdb.org/ . Video Abstract.

Potential syntrophic associations in anaerobic naphthenic acids biodegrading consortia inferred with microbial interactome networks

Naphthenic acids (NAs) can be syntrophically metabolized by indigenous microbial communities in pristine sediments beneath oil sands tailings ponds. Syntrophy is an essential determinant of the microbial interactome, however, the interactome network in anaerobic NAs-degrading consortia has not been previously addressed due to complexity and resistance of NAs. To evaluate the impact of electron acceptors on topology of interactome networks, we inferred two microbial interactome networks for anaerobic NAs-degrading consortia under nitrate- and sulfate-reducing conditions. The complexity of the network was higher under sulfate-reducing conditions than nitrate-reducing conditions. Differences in the taxonomic composition between the two modules implies that different potential syntrophic interactions exist in each network. We inferred the presence of the same syntrophic microorganisms, from genera Bellilinea, Longilinea, and Litorilinea, initiating the metabolism in both networks, but within each network, we predicted unique syntrophic associations that have not been reported. Electron acceptor has a large effect on the interactome networks for anaerobic NAs-degrading consortia, offers insight into an unrecognized dimension of these consortia. These results provide a novel approach for exploring potential syntrophic relationships in biodegrading processes to help cost-effectively remove NAs in oil sands tailings ponds.

Profiling the composition and metabolic activities of microbial community in fermented grain for the Chinese strong-flavor Baijiu production by using the metatranscriptome, high-throughput 16S rRNA and ITS gene sequencings

The composition and function of microbial community analyzed by sequencing 16S rRNA/ITS gene amplicons (DNA level) were compared with those derived by using metatranscriptome sequencing (RNA level) from the same fermented grain (FG) sample, which obtained from the key fermentation time point during the Chinese strong-flavor Baijiu (CSFB) production process. The results showed that the fungi with the highest relative abundance was Saccharomyces (RNA: 83.15%, DNA: 89.74%) at the two levels. The most abundant bacterium was Kroppenstedtia (37.09%) detected only at the DNA level, while it was Streptococcus (93.75%) at the RNA level, indicating that the structures of prokaryotic communities at the two levels were quite different. For the microbial functions, a large proportion of genes of FG microorganisms related to "Metabolism" function were observed both by using PICRUSt2 analysis (DNA level) and metatranscriptome analysis (RNA level), and especially enriched in "Carbohydrate metabolism". While the proportions of genes involved in some functions were different, such as "Replication and repair", "Membrane transport" and "Environmental adaptation", with high proportions of genes involved in at the DNA level when compared those at the RNA level. Furthermore, Saccharomyces cerevisiae was the most active microbe in the top15 pathways, followed by Torulaspora dellbrueckii. During the conversion of starch to ethanol, S. cerevisiae showed high metabolic capacity, and cooperated with other microorganisms to convert pyruvate to acetaldehyde directly or through acetyl-CoA and acetate, and then acetaldehyde to ethanol. As far as we know, this is a first study to profile the microbial community and metabolic features in FG of CSFB by using a combination of DNA- and RNA- based technologies. Our findings could provide useful insights for further understanding the active microbial function, metabolic pathways and fermentation mechanism in the FG ecosystem during CSFB fermentation.

Metagenomic analysis of soil microbial community under PFOA and PFOS stress

Perfluorinated compounds (PFCs) contamination of soil has attracted global attention in recent years but influences of PFCs on microorganisms in the soil environment have not been fully described. In this study, the effects of perfluorooctane sulphonate (PFOS) and perfluoroctanoic acid (PFOA) on bacterial communities were determined by Illumina Miseq sequencing and Illumina Hiseq Xten. The stimulation of PFCs pollutants on soil bacterial richness and community diversity were observed. Sequencing information indicated that Proteobacteria, Acidobacteria, Actinobacteria, Chloroflexi, Firmicutes, and Gemmatimonadetes were the dominant bacterial phyla. Two genera, Bacillus and Sphingomonas, exhibited adverse responses toward PFCs pollution. Carbohydrate-active enzymes (CAZy), Kyoto Encyclopedia of Genes and Genomes (KEGG) and NCBI databases were used to elucidate the proteins and function action of soil microbial to PFCs pollution. Pathways such as Carbohydrate metabolism, Global and overview maps and Membrane transport in the soil microbes were affected by PFCs stress. CAZy analysis revealed that glycosyl transferases (GTs) in PFCs-polluted soils showed more active, while glycoside hydrolases (GHs) were inhibited severely.

Insights into the effect of different levels of crude oil on hydrolyzed polyacrylamide biotransformation in aerobic and anoxic biosystems: Bioresource production, enzymatic activity, and microbial function

The differences of crude oil recovery ratio resulted in different levels of crude oil in actual hydrolyzed polyacrylamide (HPAM)-containing wastewater. The effect of crude oil on HPAM biotransformation was explored from bioresource production, enzymatic activity and microbial function. In aerobic biosystems, the highest polyhydroxyalkanoate (PHA) yield (19.6%-40.2%) and dehydrogenase (DH) activity (4.06-8.32 mg·g^-1 VSS) occurred in the 48th hour, and increased with crude oil concentration (0-400 mg·L^-1). In anoxic biosystems, the highest PHA yield (24.5%-50.5%) and DH activity (3.24-6.69 mg·g^-1 VSS) occurred in the 72nd hour, and increased with crude oil concentration. The higher substrate removal (38.5%-65.7%) occurred in aerobic biosystems, while the higher PHA accumulation occurred in anoxic biosystems. PHA yield, DH activity and HPAM removal were related. Microbial function related to HPAM biodegradation and PHA synthesis was discussed. The main function of Pseudomonas and Bacillus in aerobic biosystems was to degrade HPAM, and in anoxic biosystems was to synthesize PHA.

Hydrothermal treatment of Chlorella sp.: Influence on biochemical methane potential, microbial function and biochemical metabolism

This study focused on the effect of hydrothermal treatment (HTT) on biochemical methane potential (BMP) of Chlorella sp. The BMP was in the range of 119.16-485.90 mLCH₄/gVS, and increased by 80.31%-210.16% after HTT, while reduced 23.94% at hydrothermal treatment severity (HTS) 5.21. The cell wall was more greatly disrupted with increasing HTS, accompanied with the increase of volatile fatty acids (VFAs) and fermentation inhibitors (5-HMF and more complex chemical compositions) recoveries. The reducing sugar yields were 0.94-3.65% and obtained its maximum at a retention time of 30 min. Illumina MiSeq sequencing clarified that, the phylum Chloroflexi with functions of hydrolysis and acidogenesis, decreased with increasing HTS. The family Methanosaetaceae belonging to acetoclastic methanogens, had an unexpected decrease at HTS 5.21. As the response, VFAs concentration was less than 1 g/L after biochemical metabolism, while high concentrations of VFAs and inhibitors at HTS 5.21 led to the poor performance.

Identification of biofilm formation and exoelectrogenic population structure and function with graphene/polyanliline modified anode in microbial fuel cell

Improving anode configuration with polymer or nanomaterial modification is promising for enhancing microbial fuel cell performance. However, how anode modification affects biofilm development and electrogenic function remains poorly understood. In this study, the carbon cloth anode modified with polyaniline and reduced graphene oxide was successfully fabricated which obtained the highest power output. Accelerated electrogenic biofilm formation and the better electrogenic bacterial colonization based on the superior material properties (preferable electrochemical characteristics, the film-like structure and the more activated sites) were observed with the in situ biofilm development monitoring. The acclimation time was 2.4 times shorter with graphene and polyaniline modified anode than the bare one when inoculated with wastewater. Biofilm structure and function analysis show that Geobacter is the most predominant with the abundance as high as 81.4%, and meanwhile, electrogenesis related outer-surface octaheme c-type cytochrome omcZ is highly expressed in the modified anode. The anode modified with graphene and polyaniline favors Geobacter colonization, accelerates electrogenic biofilm formation and improves omcZ expression level, eventually leading to the improved performance of microbial fuel cell. The study for the first time reveals the impacts on biofilm development and microbial function by anode modification, which will better guide the potential application of microbial fuel cell for wastewater recovery.

A concise review of biochar application to agricultural soils to improve soil conditions and fight pollution

Application of biochar to soil can play a significant role in the alteration of nutrients dynamics, soil contaminants as well as microbial functions. Therefore, strategic biochar application to soil may provide agronomic, environmental and economic benefits. Key environmental outcomes may include reduced availability of toxic metals and organic pollutants, reduced soil N losses and longer-term storage of carbon in soil. The use of biochar can certainly address key soil agronomic constraints to crop production including Al toxicity, low soil pH and may improve nutrient use efficiency. Biochar application has also demerits to soil properties and attention should be paid when using a specific biochar for a specific soil property improvement. This review provides a concise assessment and addresses impacts of biochar on soil properties.

Complete genome sequence provides insights into the biodrying-related microbial function of Bacillus thermoamylovorans isolated from sewage sludge biodrying material

To enable the development of microbial agents and identify suitable candidate used for biodrying, the existence and function of Bacillus thermoamylovorans during sewage sludge biodrying merits investigation. This study isolated a strain of B. thermoamylovorans during sludge biodrying, submitted it for complete genome sequencing and analyzed its potential microbial functions. After biodrying, the moisture content of the biodrying material decreased from 66.33% to 50.18%, and B. thermoamylovorans was the ecologically dominant Bacillus, with the primary annotations associated with amino acid transport and metabolism (9.53%) and carbohydrate transport and metabolism (8.14%). It contains 96 carbohydrate-active- enzyme-encoding gene counts, mainly distributed in glycoside hydrolases (33.3%) and glycosyl transferases (27.1%). The virulence factors are mainly associated with biosynthesis of capsule and polysaccharide capsule. This work indicates that among the biodrying microorganisms, B. thermoamylovorans has good potential for degrading recalcitrant and readily degradable components, thus being a potential microbial agent used to improve biodrying.

Biochar lowers ammonia emission and improves nitrogen retention in poultry litter composting

The poultry industry produces abundant quantities of nutrient-rich litter, much of which is composted before use as a soil amendment. However, a large proportion of nitrogen (N) in poultry litter is lost via volatilisation during composting, with negative environmental and economic consequences. This study examined the effect of incorporating biochar during composting of poultry litter on ammonia (NH₃) volatilisation and N retention. Biochars produced at 550°C from greenwaste (GWB) and poultry litter (PLB) feedstocks were co-composted with a mixture of raw poultry litter and sugarcane straw [carbon (C):N ratio 10:1] in compost bins. Ammonia emissions accounted for 17% of the total N (TN) lost from the control and 12-14% from the biochar-amended compost. The TN emitted as NH₃, as a percentage of initial TN, was significantly lower (P<0.05) i.e. by 60% and 55% in the compost amended with GWB and PLB, respectively, relative to the control. The proportion of N retained in the finished compost, as a percentage of initial TN, was 84%, 78% and 67% for the GWB, PLB and nil biochar control, respectively. Lower concentration of dissolved organic C (DOC) together with higher activity of beta-glucosidase and leucine-aminopeptidase were found in the GWB-amended compost (cf. control). It is hypothesized that lower NH₃ emission in the GWB-amended compost was caused not just by the higher surface area of this biochar but could also be related to greater incorporation of ammonium (NH₄⁺) in organic compounds during microbial utilisation of DOC. Furthermore, the GWB-amended compost retained more NH₄⁺ at the end of composting than the PLB-amended compost. Results showed that addition of biochar, especially GWB, generated multiple benefits in composting of poultry litter: decrease of NH₃ volatilisation, decrease in NH₃ toxicity towards microorganisms, and improved N retention, thus enhancing the fertiliser value of the composted litter. It is suggested that the latter benefit is linked to a beneficial modification of the microbial environment.

Environmental drivers of soil microbial community structure and function at the Avon River Critical Zone Observatory

The Critical Zone is defined as the thin, permeable layer from the tops of the trees to the bottom of the bedrock that sustains terrestrial life on Earth. The geometry and shape of the various weathering zones are known as the critical zone architecture. At the centre of the Critical Zone are soils and the microorganisms that inhabit them. In Western Australia, the million-year-old stable weathering history and more recent lateral erosion during the past hundreds of thousands of years have created a geomorphic setting where deep weathering zones are now exposed on the surface along the flanks of many lateritic hills. These old weathering zones provide diverse physical and chemical properties that influence near surface pedologic conditions and thus likely shape current surface microbiology. Here, we present data derived from a small lateritic hill on the UWA Farm Ridgefield. Spatial soil sampling revealed the contrasting distribution patterns of simple soil parameters such as pH (CaCl2) and electric conductivity. These are clearly linked with underlying changes of the critical zone architecture and show a strong contrast with low values of pH3.3 at the top of the hill to pH5.3 at the bottom. These parameters were identified as major drivers of microbial spatial variability in terms of bacterial and archaeal community composition but not abundance. In addition, we used sensitive (14)C labelling to assess turnover of three model organic nitrogen compounds - an important biogeochemical functional trait relating to nutrient availability. Though generally rapid and in the order of rates reported elsewhere (t½<5h), some points in the sampling area showed greatly reduced turnover rates (t½>10h). In conclusion, we have shown that the weathering and erosion history of ancient Western Australia affects the surface pedology and has consequences for microbial community structure and function.

Biochar affects soil organic matter cycling and microbial functions but does not alter microbial community structure in a paddy soil

The application of biochar (BC) in conjunction with mineral fertilizers is one of the most promising management practices recommended to improve soil quality. However, the interactive mechanisms of BC and mineral fertilizer addition affecting microbial communities and functions associated with soil organic matter (SOM) cycling are poorly understood. We investigated the SOM in physical and chemical fractions, microbial community structure (using phospholipid fatty acid analysis, PLFA) and functions (by analyzing enzymes involved in C and N cycling and Biolog) in a 6-year field experiment with BC and NPK amendment. BC application increased total soil C and particulate organic C for 47.4-50.4% and 63.7-74.6%, respectively. The effects of BC on the microbial community and C-cycling enzymes were dependent on fertilization. Addition of BC alone did not change the microbial community compared with the control, but altered the microbial community structure in conjunction with NPK fertilization. SOM fractions accounted for 55% of the variance in the PLFA-related microbial community structure. The particulate organic N explained the largest variation in the microbial community structure. Microbial metabolic activity strongly increased after BC addition, particularly the utilization of amino acids and amines due to an increase in the activity of proteolytic (l-leucine aminopeptidase) enzymes. These results indicate that microorganisms start to mine N from the SOM to compensate for high C:N ratios after BC application, which consequently accelerate cycling of stable N. Concluding, BC in combination with NPK fertilizer application strongly affected microbial community composition and functions, which consequently influenced SOM cycling.

Illumina MiSeq investigations on the changes of microbial community in the Fusarium oxysporum f.sp. cubense infected soil during and after reductive soil disinfestation

Although reductive soil disinfestation (RSD) is increasingly used for the control of soil-borne diseases, its impact on the soil microbial community during and after RSD remains poorly understood. MiSeq pyrosequencing, real-time PCR and denaturing gradient gel electrophoresis were performed to investigate the changes of microbial community in the Fusarium oxysporum f. sp. cubense (FOC) infected soil during RSD and at the simulative banana cultivation after RSD. The results showed that RSD significantly increased soil microbial populations and a different microbial community with the pathogenic soil was established after RSD. Specifically, the number of Firmicutes mainly containing Ruminococcus and Coprococcus followed by a small part of Clostridium which were the dominant bacterial genera significantly increased during RSD. In contrast, Symbiobacterium and Flavisolibacter were the dominant genera in the flooding soil. When the soils were recovered under aerobic condition, the relative abundances of the bacteria belonging to the phylum Bacteroidetes, Acidobacteria, Planctomycetes increased as alternatives to the reducing Firmicutes. For fungi, the population of F. oxysporum significantly decreased during RSD accompanied with the pH decline, which resulted in the significant decrease of relative abundance in the phylum Ascomycota. Alternatively, the relative abundances of some other fungal species increased, such as Chaetomium spp. and Penicillium spp. belonging to Ascomycota and the family Clavulinaceae belonging to Basidiomycota. Then, the relative abundance of Ascomycota re-increased after RSD with Podospora and Zopfiella as dominant genera, whereas the relative abundance of Fusarium further decreased. Overall, the microbial populations and community re-established by RSD made the soil more disease-suppressive and beneficial to the soil nutrient cycling and plant growth compared with the previous pathogenic soil.