Defluorination of monofluorinated alkane by Rhodococcus sp. NJF-7 isolated from soil.

Microbial degradation of fluorinated compounds raised significant attention because of their widespread distribution and potential environmental impacts. Here, we report a bacterial isolate, Rhodococcus sp. NJF-7 capable of defluorinating monofluorinated medium-chain length alkanes. This isolate consumed 2.29 ± 0.13 mmol L- 1 of 1-fluorodecane (FD) during a 52 h incubation period, resulting in a significant release of inorganic fluoride amounting to 2.16 ± 0.03 mmol L- 1. The defluorination process was strongly affected by the initial FD concentration and pH conditions, with lower pH increasing fluoride toxicity to bacterial cells and inhibiting enzymatic defluorination activity. Stoichiometric conversion of FD to fluoride was observed at neutral pH with resting cells, while defluorination was significantly lower at reduced pH (6.5). The discovery of the metabolites decanoic acid and methyl decanoate suggests that the initial attack by monooxygenases may be responsible for the biological defluorination of FD. The findings here provide new insights into microbial defluorination processes, specifically aiding in understanding the environmental fate of organic semi-fluorinated alkane chemicals.

Critical insights into the Hormesis of antibiotic resistome in saline soil: Implications from salinity regulation.

Soil is recognized as an important reservoir of antibiotic resistance genes (ARGs). However, the effect of salinity on the antibiotic resistome in saline soils remains largely misunderstood. In this study, high-throughput qPCR was used to investigate the impact of low-variable salinity levels on the occurrence, health risks, driving factors, and assembly processes of the antibiotic resistome. The results revealed 206 subtype ARGs across 10 categories, with medium-salinity soil exhibiting the highest abundance and number of ARGs. Among them, high-risk ARGs were enriched in medium-salinity soil. Further exploration showed that bacterial interaction favored the proliferation of ARGs. Meanwhile, functional genes related to reactive oxygen species production, membrane permeability, and adenosine triphosphate synthesis were upregulated by 6.9%, 2.9%, and 18.0%, respectively, at medium salinity compared to those at low salinity. With increasing salinity, the driver of ARGs in saline soils shifts from bacterial community to mobile gene elements, and energy supply contributed 28.2% to the ARGs at extreme salinity. As indicated by the neutral community model, stochastic processes shaped the assembly of ARGs communities in saline soils. This work emphasizes the importance of salinity on antibiotic resistome, and provides advanced insights into the fate and dissemination of ARGs in saline soils.

Coupling between 2, 2', 4, 4'-tetrabromodiphenyl ether (BDE-47) debromination and methanogenesis in anaerobic soil microcosms.

Polybrominated diphenyl ethers (PBDEs) are persistent pollutants that may undergo microbial-mediated debromination in anoxic environments, where diverse anaerobic microbes such as methanogenic archaea co-exist. However, current understanding of the relations between PBDE pollution and methanogenic process is far from complete. To address this knowledge gap, a series of anaerobic soil microcosms were established. BDE-47 (2, 2', 4, 4'-tetrabromodiphenyl ether) was selected as a model pollutant, and electron donors were supplied to stimulate the activity of anaerobes. Debromination and methane production were monitored during the 12 weeks incubation, while obligate organohalide-respiring bacteria (OHRBs), methanogenic, and the total bacterial communities were examined at week 7 and 12. The results demonstrated slow debromination of BDE-47 in all microcosms, with considerable growth of Dehalococcoides and Dehalogenimonas over the incubation observed in most BDE-47 spiked treatments. In addition, the accumulation of intermediate metabolites positively correlated with the abundance of Dehalogenimonas at week 7, suggesting potential role of these OHRBs in debromination. Methanosarcinaceae were identified as the primary methanogenic archaea, and their abundance were correlated with the production of debrominated metabolites at week 7. Furthermore, it was observed for the first time that BDE-47 considerably enhanced methane production and increased the abundance of mcrA genes, highlighting the potential effects of PBDE pollution on climate change. This might be related to the inhibition of reductive N- and S-transforming microbes, as revealed by the quantitative microbial element cycling (QMEC) analysis. Overall, our findings shed light on the intricate interactions between PBDE and methanogenic processes, and contribute to a better understanding of the environmental fate and ecological implication of PBDE under anaerobic settings.

Dosage and exposure time effects of two micro(nono)plastics on arbuscular mycorrhizal fungal diversity in two farmland soils planted with pepper (Capsicum annuum L.).

As emerging environmental pollutants, micro(nano)plastics (MPs) like polyethylene terephthalate (PET) and low-density polyethylene (LDPE) have adverse effects on terrestrial biota and ecosystem function. However, the performance and roles of soil arbuscular mycorrhizal (AM) fungi in MPs-contaminated vegetable fields are poorly understood. Thus, a 120-day pot experiment was conducted to test the impacts of two input levels of either PET (~13 µm) or LDPE (~500 nm) on AM fungal diversity and pepper (Capsicum annuum L.) growth in two farmland soils collected from Nanjing (NJ) and Chongqing (CQ), respectively. In the vast majority of cases, 1 % rather than 0.1 % of both MPs greatly decreased the observed richness, Shannon and Simpson's indices, and Pielou's evenness of AM fungi, and decreased mycorrhizal colonization, root and shoot biomasses, fruit yield, and leaf superoxide dismutase, peroxidase, and catalase activities of pepper, while increased leaf malondialdehyde content. From day 40 to 120, the inhibition of either diversity or vitality of AM fungi by 1 % and 0.1 % of MPs gradually increased and weakened, respectively. Compared with PET, LDPE with substantially smaller particle size was more toxic to mycorrhization at day 40, but no longer at day 120. Almost all plant parameters significantly correlated to mycorrhizal colonization, which significantly correlated to both Shannon and Simpson's indices of AM fungi, and soil pH, available P and K concentrations, and alkaline phosphatase activity. All diversity indices of AM fungi clearly negatively correlated to soil pH from 4.4 to 5.6 for the NJ soil and from 5.3 to 6.5 for the CQ soil, and also positively to mineral N and negatively to available P concentrations for the NJ and CQ soils, respectively. Thus, the study emphasized that high input of MPs significantly inhibited soil AM fungal diversity and vitality and thereby vegetable growth via changing soil pH and major nutrient availability.

Comparison of bacterial and fungal communities structure and dynamics during chicken manure and pig manure composting.

Composting is a sustainable and eco-friendly technology that turns animal waste into organic fertilizers. It remains unclear whether differences exist in the structure of microbial communities during different livestock manure composting. This study analyzed the dynamic change of bacterial and fungal communities, metabolic function, and trophic mode during chicken manure (CM) and pig manure (PM) composting based on 16S rRNA and ITS sequencing. Environmental factors were investigated for their impact on microbial communities. During composting, bacterial diversity decreased and then increased, while fungal diversity slightly increased and then decreased. Saccharomonospora and Aspergillus were the dominant genera and key microorganisms in CM and PM, respectively, which played crucial roles in sustaining the stability of the ecological network structure in the microbial ecology and participating in metabolism. Saccharomonospora gradually increased, while Aspergillus increased at first and then decreased. PM had better microbial community stability and more keystone taxa than CM. In CM and PM, the primary function of bacterial communities was metabolism, while saprotroph was the primary trophic mode of fungal communities. Dissolved organic carbon (DOC) was the primary factor influencing the structure and function of microbial communities in CM and PM. In addition to DOC, pH and moisture were important factors affecting the fungal communities in CM and PM, respectively. These results show that the succession of bacteria and fungi in CM and PM proceeded in a similar pattern, but there are still some differences in the dominant genus and their responses to environmental factors.

Low-temperature thermally enhanced bioremediation of polycyclic aromatic hydrocarbon-contaminated soil: Effects on fate, toxicity and bacterial communities.

Remediation of polycyclic aromatic hydrocarbon (PAH)-contaminated soil using thermal desorption technology typically requires very high temperatures, necessitating coupled microbial treatment for energy and cost reduction. This study investigated the fate and toxicity of PAHs as well as the responses of microbial communities following thermal treatment within a low temperature range. The optimal temperature for PAH mineralization was 20-28 °C, within the growth range of most mesophilic microorganisms. By contrast, 50 °C treatment almost completely inhibited PAH mineralization but resulted in the greatest detoxification effect particularly for cardiotoxicity and nephrotoxicity. A potential increase in toxicity was observed at 28 °C. Co-metabolism and non-extractable residue formation may play an interdependent role in thermally enhanced bioremediation. Moreover, alterations in bacterial communities were strongly associated with PAH mineralization and zebrafish toxicity, revealing that soil microorganisms play a direct role in PAH mineralization and served as ecological receptors reflecting changes in toxicity. Network analysis revealed that Firmicutes formed specific ecological communities at high temperature, whereas Acidobacteria and Proteobacteria act as primary PAH degraders at moderate temperature. These findings will enable better integration of strategies for thermal and microbial treatments in soil remediation.

Impact of lignin constituents on the bacterial community and polycyclic aromatic hydrocarbon co-metabolism in an agricultural soil.

Lignin is a complex biopolymer comprising phenolic monomers with different degrees of methoxylation and may potentially enhance the degradation of soil pollutants such as polycyclic aromatic hydrocarbons (PAHs) through co-metabolism. However, the contribution of lignin constituents, including phenolic and methoxy subunits, to PAH biodegradation remains unclear. Here, p-hydroxybenzoate (pHBA), vanillate and methanol were selected to simulate phenolic units and methoxy groups of lignin. Soil microcosms receiving these compounds were established to evaluate their regulation on the bacterial community and PAH co-metabolism. There were different effects of different components on the biodegradation of a four-ring PAH, benzo(a)anthracene (BaA), as characterized using an isotopic tracer. Only vanillate significantly stimulated BaA mineralization to CO2, with pHBA and methanol leading to no appreciable change in the allocation of BaA in soil compartments. The lignin constituents had differential impacts on the soil bacterial community, with substantial enrichment of methylotrophs occurring in methanol-supplemented microcosms. Both vanillate and pHBA selected several aromatic degraders. Vanillate caused additional enrichment of methylotrophs, suggesting structure-dependent stimulation of bacterial functional guilds by lignin monomers. Compared with its constituents, lignin produced more extensive responses in terms of bacterial diversity and composition and the fate of BaA. However, it was difficult to link BaA co-metabolism to any specific bacterial taxa in the presence of lignin or its subunits. The results indicate that the co-metabolism effects of lignin may not be directly associated with phenolic or methoxy metabolism but with its regulation of the soil microbiome.

Soil drying legacy does not affect phenanthrene fate in soil but modifies bacterial community response.

Alteration of the structure of soil microbial communities following the elimination of hydrophobic organic pollutants (e.g., polycyclic aromatic hydrocarbons, PAHs) is generally assessed using DNA-based techniques, and soil is often required to dry prior to pollutant addition, to facilitate a better mix when establishing microcosms. However, the drying practice may have a legacy effect on soil microbial community structure, which would in turn influence the biodegradation process. Here, we used 14C-labeled phenanthrene to examine the potential side effects of precedent short-term drought events. The results indicate that the drying practice had legacy effects on soil microbial community structure, illustrated by irreversible shifts in the communities. The legacy effects had no significant impact on phenanthrene mineralization and non-extractable residue formation. However, they altered the response of bacterial communities to PAH degradation, leading to a decrease in the abundance of potential PAH degradation genes plausibly attributed to moderately abundant taxa. Based on a comparison of the varied effects of different drying intensity levels, an accurate description of microbial responses to phenanthrene degradation strongly relies on the establishment of stable microbial communities before PAH amendment. Concurrent alterations in the communities resulting from environmental perturbation could greatly mask minor alterations from the degradation of recalcitrant hydrophobic PAH. In practice, to minimize the legacy effects, a soil equilibration step with a reduced drying intensity is indispensable.

[Dynamic Changes in Antibiotic Resistance Genes During Biological Fermentation of Chicken Manure and Pig Manure].

Livestock manure is a major carrier that stores and transmits antibiotic resistance genes (ARGs). The aim of this study was to identify the crucial environmental factors that result in the change in relative abundance of ARGs and MGEs to explore effective methods to reduce the occurrence of ARGs. The abundance of ten ARGs and five MGEs were measured using real-time quantitative PCR with 0, 3, 7, 10, 14, 21, 28, 45, 60, and 75 d in CM and PM aerobic composting. The succession law of the bacterial community was analyzed using 16S rRNA high-throughput sequencing. Furthermore, the abundance of ARGs and MGEs was correlated with the properties (temperature, moisture content, pH, and DOC) of composting piles to identify the crucial factors affecting the variation in ARGs and MGEs. The results showed that the abundance of ARGs and MGEs in PM was higher than that in CM. Composting significantly reduced the relative abundance of nine ARGs and five MGEs. The removal ratios of three ARGs (tetM, tetT, and aacA) and four MGEs (ISEcp1, IS1216, IS613, and tnp614) in CM reached 99%. The removal ratios of nine ARGs[tetB(P), tetL, tetM, tetO, tetT, aacA, aadD,aphA3, and sat4] and four MGEs (ISEcp1, IS26, IS1216, and tnp614) reached 99% in PM. However, the abundance of the genes tetG, intI1, and IS6100 increased. Firmicutes and Actinobacteria were dominant in CM and PM during composting. Actinobacteria and Proteobacteria may have been the major host bacteria of tetG and intI1. The redundancy analysis showed that moisture and pH were the crucial factors that could influence the differences in the abundance of ARGs and MGEs. The composition and abundance of ARGs were driven by physicochemical properties, bacterial community, and MGEs. Composting could significantly reduce the abundance of ARGs in CM and PM, thus reducing the risk of ARGs being distributed via livestock manure application. However, some ARGs and MGEs remained in high abundance. Therefore, it is necessary to further optimize the composting process, improve the harmless treatment effect of livestock manure, and promote the safe agricultural use of organic fertilizers.

Contrasting responses of bacterial community to 4,4'-dibromodiphenyl ether (BDE-15) contamination in soil microcosms at different temperatures.

Polybrominated diphenyl ethers (PBDEs) are biodegradable organic pollutants and pose potential risks to microorganisms exposed to the contamination, which are also affected by a variety of factors, such as temperature, in real environmental settings. A better understanding of the microbial community responses to PBDEs at different temperatures has practical significance for assessing ecological risks or possible degraders of these widely used flame retardants. In this study, soil microcosms spiked with or without 100 mg kg-1 4,4'-dibromodiphenyl ether (BDE-15) were established and incubated at four different temperatures (4 °C, 20 °C, 37 °C, and varying ambient temperature) for up to 180 days. Concentration and carbon isotope analyses were used to verify the transformation of BDE-15. Bacterial communities were monitored during the incubation to evaluate the community succession under the PBDE stress. The results showed the majority of added BDE-15 remained after the incubation period, with limited degradation occurred at all four temperatures. Temperature significantly shaped the richness, diversity, composition and co-occurrence network of soil bacterial community, while the impacts of PBDE on soil bacteria were temperature dependent. When incubated at 4 °C, BDE-15 substantially reduced the network complexity and changed the ratio of negative to positive interactions between taxa (nodes), highlighting the PBDE-associated risks at low temperature. At higher temperatures, BDE-15 had negligible influence on the community characteristics and network. Random forest model identified distinct taxa that might be related to PBDE degradation at different incubation temperatures. These findings demonstrate contrasting bacterial community effects of PBDE at different temperatures, thus attention should be paid to the ecological impacts of soil pollution under real environmental conditions.

Persistence of Salmonella Typhimurium and antibiotic resistance genes in different types of soil influenced by flooding and soil properties.

Salmonella is a zoonotic foodborne bacterial pathogen that can seriously harm health. Persistence of Salmonella and antibiotic resistance genes (ARGs) in different types of soil under flooding and natural conditions are rare explored. This study investigated the dynamic changes of the Salmonella, ARGs and bacterial communities in three types of soils applied with pig manure in lab scale. Abundance of the Salmonella Typhimurium in soils reduced to the detection limit varied from 40 to 180 days, most of the Salmonella did not survive in soil for more than 90 days. Flooding and soil texture (content of sand) promote the decline rate of Salmonella. No Salmonella was found have acquired resistance gene from the soil or manure after 90 days. 64 ARGs and 11 MGEs were quantified, abundance of these genes and risky ARGs both gradually decline along with the extension of time. Most of the extrinsic ARGs cannot colonize in soil, cellular protection and antibiotic deactivation were their main resistance mechanism. Multidrug resistance and efflux pump were the dominant class and mechanism of soil intrinsic ARGs. Flooding can affect the ARGs profiles by reducing the types of extrinsic ARGs invaded into soil and inhibit the proliferation of intrinsic genes. Soil sand content, soil moisture and nutrition concentrations had significant direct effect on the abundance or profile of ARGs. Soil bacterial community structures also changed along with the extension of time and affected by flooding. Network analyses between ARGs and bacteria taxa revealed that Actinobacteria and Myxococcia were the main hosts of intrinsic ARGs, some taxa may play a role in inhibiting extrinsic ARGs colonization in the soils. These findings unveil that saturate soil with water may play a positive role in reducing potential risk of Salmonella and ARGs in the farmland environment.

Distribution of antibiotic, heavy metals and antibiotic resistance genes in livestock and poultry feces from different scale of farms in Ningxia, China.

With the rapid development of livestock and poultry breeding industries, pollution problems caused by the discharge of animal feces have become increasingly severe. Nevertheless, there are limited investigations about nutrients and pollutants in animal feces from different scale of farms, especially in Northwest China. Here we investigated nutrients content, 19 antibiotics, 7 heavy metals, 329 antibiotic resistance genes (ARGs) and 35 mobile genetic elements (MGEs) in six main livestock and poultry feces collected from 5 coastal regions of Ningxia. Pig and chicken feces exhibited higher levels of nutrients content, but antibiotics, heavy metals, ARGs and MGEs were also more abundant than those in cattle and sheep feces. Chlortetracycline hydrochloride and doxycycline hyclate were the most commonly used antibiotic, which detected with the highest rate and concentrations, especially in broiler, layer and pig feces. Strong positive correlations were found among different ARGs or between ARGs and MGEs, indicated the risk of horizontal gene transfer of ARGs. Residual antibiotic and heavy metals significantly affect the abundance of ARGs. Feeding mode and the scales of the animal farms served little effect on the distribution of the pollutants (including residual antibiotics, heavy metals, MGEs and ARGs), which were significantly different among animal types. Use of antibiotics and heavy metals should be strictly regulated, especially in chicken and pig farms, in order to control contaminants and reduce potential risks to the environment.

Resistance and resilience of soil bacterial community to zero-valent iron disposal of lindane contamination.

Zero-valent iron (ZVI, Fe0) enables chemical reduction of environmental pollutants coupled with reactivity loss due to surface oxidation. During ZVI treatment process, however, microbial community stability in terms of resistance and resilience remains largely unclear. Here, we monitored bacterial community succession over a 4 weeks period in soil microcosms with or without 2% (w/w) Fe0 amendment. To simulate soil pollution, 100 µg g-1 chlorinated pesticide lindane (γ-hexachlorocyclohexane) was added to the microcosms as a model contaminant. In addition to microbial activity as measured by soil organic carbon mineralization, bacterial abundance, diversity and composition were determined using qPCR and high-throughput sequencing of 16 S rRNA genes. Co-occurrence analysis was performed to reveal the interaction patterns within the bacterial communities. The results indicated that ZVI caused near-complete transformation of lindane, while in the microcosms without Fe0 amendment the pesticide was recalcitrant. ZVI strongly inhibited CO2-efflux at the early stage of incubation, but the bacterial community appeared to be less sensitive to Fe0 amendment. The ratios of negative to positive correlations between network nodes suggested that Fe0 had marginal influence on community stability compared to the lindane treatments, which destabilized the bacterial community. Community succession occurred in the presence of ZVI, as exemplified by a dominancy transition from anaerobic to aerobic taxa. Yet, ZVI alleviated the stress of lindane on soil bacteria by improving community structure and increasing network complexity. Taken together, these findings demonstrate the stability of soil bacterial community under Fe0 stress, which might be conducive to functional recovery of soil microorganisms following ZVI remediation.

Beyond the snapshot: identification of the timeless, enduring indicator microbiome informing soil fertility and crop production in alkaline soils.

BACKGROUND: Microorganisms are known to be important drivers of biogeochemical cycling in soil and hence could act as a proxy informing on soil conditions in ecosystems. Identifying microbiomes indicative for soil fertility and crop production is important for the development of the next generation of sustainable agriculture. Earlier researches based on one-time sampling have revealed various indicator microbiomes for distinct agroecosystems and agricultural practices as well as their importance in supporting sustainable productivity. However, these microbiomes were based on a mere snapshot of a dynamic microbial community which is subject to significant changes over time. Currently true indicator microbiomes based on long-term, multi-annual monitoring are not available. RESULTS: Here, using samples from a continuous 20-year field study encompassing seven fertilization strategies, we identified the indicator microbiomes ecophysiologically informing on soil fertility and crop production in the main agricultural production base in China. Among a total of 29,184 phylotypes in 588 samples, we retrieved a streamlined consortium including 2% of phylotypes that were ubiquitously present in alkaline soils while contributing up to half of the whole community; many of them were associated with carbon and nutrient cycling. Furthermore, these phylotypes formed two opposite microbiomes. One indicator microbiome dominated by Bacillus asahii, characterized by specific functional traits related to organic matter decomposition, was mainly observed in organic farming and closely associated with higher soil fertility and crop production. The counter microbiome, characterized by known nitrifiers (e.g., Nitrosospira multiformis) as well as plant pathogens (e.g., Bacillus anthracis) was observed in nutrient-deficit chemical fertilizations. Both microbiomes are expected to be valuable indictors in informing crop yield and soil fertility, regulated by agricultural management. CONCLUSIONS: Our findings based on this more than 2-decade long field study demonstrate the exciting potential of employing microorganisms and maximizing their functions in future agroecosystems. Our results report a "most-wanted" or "most-unwanted" list of microbial phylotypes that are ready candidates to guide the development of sustainable agriculture in alkaline soils.

Microbial Community Composition and Activity in Saline Soils of Coastal Agro-Ecosystems.

Soil salinity is a serious problem for agriculture in coastal regions. Nevertheless, the effects of soil salinity on microbial community composition and their metabolic activities are far from clear. To improve such understanding, we studied microbial diversity, community composition, and potential metabolic activity of agricultural soils covering non-, mild-, and severe-salinity. The results showed that salinity had no significant effect on bacterial richness; however, it was the major driver of a shift in bacterial community composition and it significantly reduced microbial activity. Abundant and diverse of microbial communities were detected in the severe-salinity soils with an enriched population of salt-tolerant species. Co-occurrence network analysis revealed stronger dependencies between species associated with severe salinity soils. Results of microcalorimetric technology indicated that, after glucose amendment, there was no significant difference in microbial potential activity among soils with the three salinity levels. Although the salt prolonged the lag time of microbial communities, the activated microorganisms had a higher growth rate. In conclusion, salinity shapes soil microbial community composition and reduces microbial activity. An addition of labile organic amendments can greatly alleviate salt restrictions on microbial activity, which provides new insight for enhancing microbial ecological functions in salt-affected soils.

Organic and Inorganic Amendments Shape Bacterial Indicator Communities That Can, In Turn, Promote Rice Yield.

The dynamic patterns of the belowground microbial communities and their corresponding metabolic functions, when exposed to various environmental disturbances, are important for the understanding and development of sustainable agricultural systems. In this study, a two-year field experiment with soils subjected to: chemical fertilization (F), mushroom residues (MR), combined application of chemical fertilizers and mushroom residues (MRF), and no-fertilization (CK) was conducted to evaluate the effect of fertilization on the soil bacterial taxonomic and functional compositions as well as on the rice yield. The highest rice yield was obtained under MRF. Soil microbial properties (microbial biomass carbon (MBC), microbial biomass nitrogen (MBN), urease, invertase, acid phosphatase, and soil dehydrogenase activities) reflected the rice yield better than soil chemical characteristics (soil organic matter (SOM), total N (TN), total K (TK), available P (AP), available K (AK), and pH). Although the dominant bacterial phyla were not significantly different among fertilizations, 10 bacterial indicator taxa that mainly belonged to Actinobacteria (Nocardioides, Marmoricola, Tetrasphaera, and unclassified Intrasporangiaceae) with functions of xenobiotic biodegradation and metabolism and amino acid and nucleotide metabolism were found to strongly respond to MRF. Random Forest (RF) modeling further revealed that these 10 bacterial indicator taxa act as drivers for soil dehydrogenase, acid phosphatase, pH, TK, and C/N cycling, which directly and/or indirectly determine the rice yield. Our study demonstrated the explicit links between bacterial indicator communities, community function, soil nutrient cycling, and crop yield under organic and inorganic amendments, and highlighted the advantages of the combined chemical and organic fertilization in agroecosystems.

Synergy between fungi and bacteria promotes polycyclic aromatic hydrocarbon cometabolism in lignin-amended soil.

Lignin enhanced biodegradation of polycyclic aromatic hydrocarbons (PAHs) in soil, but collaboration among soil microorganisms during this process remains poorly understood. Here we explored the relations between microbial communities and PAH transformation in soil microcosms amended with lignin. Mineralization of the four-ring benzo(a)anthracene (BaA), which was selected as a model, was determined by using an isotope-labeled tracer. The eukaryotic inhibitor cycloheximide and redox mediator ABTS were used to validate the fungal role, while microbial communities were monitored by amplicon sequencing. The results demonstrated that lignin significantly promoted BaA mineralization to CO2, which was inhibited and enhanced by cycloheximide and ABTS, respectively. Together with the increased abundance of Basidiomycota, these observations suggested an essential contribution of fungi to BaA biodegradation, which possibly through a ligninolytic enzyme-mediated pathway. The enrichment of Methylophilaceae and Sphingomonadaceae supported bacterial utilization of methyl and aryl groups derived from lignin, implicating cometabolic BaA degradation. Co-occurrence network analysis revealed increased interactions between fungi and bacteria, suggesting they played synergistic roles in the transformation of lignin and BaA. Collectively, these findings demonstrate the importance of synergy between fungi and bacteria in PAH transformation, and further suggest that the modulation of microbial interplay may ameliorate soil bioremediation with natural materials such as lignin.

The Long-Term Effects of Using Phosphate-Solubilizing Bacteria and Photosynthetic Bacteria as Biofertilizers on Peanut Yield and Soil Bacteria Community.

Microbial inoculation is a promising strategy to improve crop yields and reduce the use of chemical fertilizers, thereby creating environment-friendly agriculture. In this study, the long-term (5 years) effects of a phosphate-solubilizing bacterium Burkholderia cepacia ISOP5, a purple non-sulfur bacterium Rhodopseudomonas palustris ISP-1, and a mixed inoculation of these two bacteria (MB) on peanut yield, soil microbial community structure, and microbial metabolic functions were evaluated in a field experiment. After 5 years of inoculation, total peanut yield with B. cepacia ISOP5, R. palustris ISP-1, and MB treatments increased by 8.1%, 12.5%, and 19.5%, respectively. The treatments also significantly promoted the absorption of N and increased the protein content in peanut seeds. Nutrient content also increased to some extent in the bacteria-inoculum-treated soil. However, bacterial community diversity and richness were not significantly affected by bacterial inoculums, and only minor changes occurred in the bacterial community composition. Functional prediction revealed that bacterial inoculums reduced the relative abundance of those genes associated with P uptake and transport as well as increased the abundance of genes associated with inorganic P solubilization and organic P mineralization. Bacterial inoculums also increased the total relative abundance of genes associated with N metabolism. In addition to developing sustainable and eco-friendly agricultural practice, crop inoculation with B. cepacia ISOP5 and R. palustris ISP-1 would improve soil fertility, enhance microbial metabolic activity, and increase crop yield.

Organic matter- and temperature-driven deterministic assembly processes govern bacterial community composition and functionality during manure composting.

Although many studies have shown that microbial communities play important roles in organic waste composting due to the involvement of specific microbial taxa with metabolic functions, the underlying ecological processes of community assembly and governing factors remain elusive. Thus, a chicken manure composting experiment as a model system of microbially mediated organic waste composting was conducted. Ecological null modeling and metabolic functional prediction combined with electrospray ionization (ESI) Fourier transform ion cyclotron resonance mass spectrometry (FT-ICR MS) were used to quantify assembly processes governing bacterial community composition and functions during composting. The results showed the predominant role of deterministic assembly processes in shifting community compositions both across and within composting stages. Stochastic assembly processes also concomitantly influenced microbial community compositions. Changes in the organic matter (OM) content and its chemical properties and temperature governed bacterial community assembly processes throughout the stages by selecting specific bacterial taxa such as Cardiobacteriales, Bacteroidales, and Lachnospiraceae on day 1, Firmicutes on days 6, 25 and 37, and Sphingobacteriales, Thermoactinomycetaceae, Actinobacteria, and Novibacillus on day 45. These taxa ultimately influenced community functions such as environmental information processing, carbohydrate and amino acid metabolism, cellular processes, and genetic information processes involved in composting. Taken together, this study indicates that deterministic assembly processes governed by OM content and quality as well as temperature influenced microbial community turnover and determined community functions during composting. These results are important for better understanding and predicting microbial-driven composting and for ultimately manipulating microorganisms for environmentally-friendly composting outcomes.