Bacterial 16S rRNA Gene Abundance Research Articles

Dicyandiamide Applications Mitigate the Destructive Effects of Graphene Oxide on Microbial Activity, Diversity, and Composition and Nitrous Oxide Emission in Agricultural Soil.

The widespread production and utilization of graphene oxide (GO) raise concerns about its environmental release and potential ecological impacts, particularly in agricultural soil. Effective nitrogen (N) management, especially through nitrification inhibitors like dicyandiamide (DCD), might mitigate the negative effects of GO exposure on soil microbes via N biostimulation. This study quantified changes in soil physicochemical properties, nitrous oxide (N2O) emissions, microbial activity, biomass, and community after treatments with GO and DCD. The GO exposure significantly reduced bacterial 16S rRNA gene abundance and the biomass of major bacterial phyla. It also stimulated pathways linked to human diseases. However, DCD application alleviated the negative effects of GO exposure on soil bacterial biomass. While DCD application significantly reduced soil N2O emission, the GO application tended to hinder the inhibiting performance of DCD. Our findings highlight the hazards of GO exposure to soil microbes and the potential mitigation strategy with soil N management.

Influence of sedimentary deposition on the microbial assembly process in Arctic Holocene marine sediments.

The sea-level rise during the Holocene (11-0 ky BP) and its resulting sedimentation and biogeochemical processes may control microbial life in Arctic sediments. To gain further insight into this interaction, we investigated a sediment core (up to 10.7 m below the seafloor) from the Chuckchi Shelf of the western Arctic Ocean using metabarcoding-based sequencing and qPCR to characterize archaeal and bacterial 16S rRNA gene composition and abundance, respectively. We found that Arctic Holocene sediments harbor local microbial communities, reflecting geochemical and paleoclimate separations. The composition of bacterial communities was more diverse than that of archaeal communities, and specifically distinct at the boundary layer of the sulfate-methane transition zone. Enriched cyanobacterial sequences in the Arctic middle Holocene (8-7 ky BP) methanogenic sediments remarkably suggest past cyanobacterial blooms. Bacterial communities were phylogenetically influenced by interactions between dispersal limitation and environmental selection governing community assembly under past oceanographic changes. The relative influence of stochastic and deterministic processes on the bacterial assemblage was primarily determined by dispersal limitation. We have summarized our findings in a conceptual model that revealed how changes in paleoclimate phases cause shifts in ecological succession and the assembly process. In this ecological model, dispersal limitation is an important driving force for progressive succession for bacterial community assembly processes on a geological timescale in the western Arctic Ocean. This enabled a better understanding of the ecological processes that drive the assembly of communities in Holocene sedimentary habitats affected by sea-level rise, such as in the shallow western Arctic shelves.

To close or open the tank input water valve: Secondary water-supply systems with double tanks will induce a higher microbial risk

Secondary water supply systems (SWSSs) are widely used to supply water to high-rise households in urban residential buildings. A special mode of double tanks with one used while another was spared was noted in SWSSs, which would facilitate microbial growth due to longer water stagnation in the spare tank. There are limited studies on the microbial risk of water samples in such SWSSs. In this study, the input water valves of the operational SWSSs consisting of double tanks were artificially closed and opened on time. Propidium monoazide-qPCR and high-throughput sequencing were performed to systematically investigate the microbial risks in water samples. After closing the tank input water valve, it may take several weeks to replace the bulk water in the spare tank. The residual chlorine concentration in the spare tank decreased by up to 85 % within 2–3 days compared with that in the input water. The microbial communities in the spare and used tank water samples clustered separately. High bacterial 16S rRNA gene abundance and pathogens-like sequences were detected in the spare tanks. Most antibiotic-resistant genes (11/15) in the spare tanks showed an increase in their relative abundance. Moreover, when both tanks within one SWSS were in use, the water quality of the used tank water samples deteriorated to varying degrees. Overall, running SWSSs with double tanks will reduce the replacement rate of water in one storage tank, and consumers who use taps served by the presented SWSSs may have a higher microbial risk.

High-throughput sequencing reveals the main drivers of niche-differentiation of bacterial community in the surface sediments of the northern South China sea

Studies on marine bacterial communities have revealed endemism in local communities, yet the underlying mechanisms remained elusive. Environmental gradient settings can benefit the straightaway study of community composition changes and the mechanisms explaining them. Here, MiSeq-based 16S rRNA gene sequencing was performed on 12 surface sediment samples from the northern South China Sea (nSCS) revealing that shallow-sea samples had a higher alpha diversity than deep-sea samples, and were differentiated from them significantly based on beta diversity. Temperature, seawater depth, and salinity were the top three influential factors. Bacterial 16S rRNA gene abundance was positively correlated with temperature, and negatively correlated with salinity. Sulfate-reducing bacteria including Desulfobacteraceae, Desulfobulbaceae, and Syntrophobacteraceae were enriched in shallow-sea sediments, co-abundant with nitrite-oxidizing Nitrospira and potential sulfur-oxidizing shallow-sea specific Woeseiaceae/JTB255 clade. Meanwhile, the co-existing and co-abundant of marine anammox and n-damo bacteria were enriched in deep-sea sediments, which was firstly evidenced in this study. The global deep-sea cosmopolitans, OM1 clade, and deep-sea specific Woeseiaceae/JTB255 clade were also found enriched in deep-sea sediments of nSCS. The discovery of novel taxa which were differentially enriched in shallow-/deep-sea sediments not only shed light on enigmatic physiological properties and the natural selection mechanism, but also provided the potential ecological-functional links which invoked further genomics-based metabolic characteristics.

Macroaggregates Serve as Micro-Hotspots Enriched With Functional and Networked Microbial Communities and Enhanced Under Organic/Inorganic Fertilization in a Paddy Topsoil From Southeastern China.

Microbial communities of soil aggregate-size fractions were explored with molecular and networking assays for topsoil samples from a clayey rice paddy under long-term fertilization treatments. The treatments included no fertilizer (NF) as control, chemical fertilizer only (CF), chemical fertilizer with swine manure (CFM), and chemical fertilizer with rice straw return (CFS). Following a wet-sieving protocol, water-stable aggregates were separated into size fractions of large macroaggregates (L-MacA, >2,000 μm), macroaggregates (MacA, 2,000–250 μm), microaggregates (MicA, 250–53 μm), fine microaggregates (F-MicA, 53–2 μm), and fine clay (F-Clay, <2 μm). Mass proportion was 32.3–38.2% for F-MicA, 23.0–31.5% for MacA, 19.0–23.1% for MicA, 9.1–12.0% for L-MacA, and 4.9–7.5% for F-Clay, respectively. The proportion of MacA was increased, but F-Clay was reduced by fertilization, whereas the mean weight diameter was increased by 8.0–16.2% from 534.8 μm under NF to 621.5 μm under CFM. Fertilization affected bacterial 16S rRNA and fungal 18S rRNA gene abundance in F-MicA and F-Clay but not in aggregates in size larger than 53 μm. However, bacterial and fungal community α-diversities and community structures were quite more divergent among the fertilization treatments in all size fractions. Organic carbon and gene abundance of bacteria and fungi were enriched in both L-MacA and MacA but depleted in F-Clay, whereas microbial Shannon diversity was rarely changed by fraction size under the four treatments. L-MacA and MacA contained more bacteria of r-strategists and copiotrophs, whereas F-MicA and F-Clay were demonstrated with a higher abundance of K-strategists and oligotrophs. Guilds of parasitic and litter saprotrophic fungi were enriched in F-MicA but depleted in L-MacA. Furthermore, most of bacterial and fungal operational taxonomic units were strongly interacted in L-MacA and MacA rather than in MicA and F-Clay. Thus, MacA acted as micro-hotspots enriched with functional and networked microbial communities, which were enhanced with organic/inorganic fertilization in the rice paddy.

Moso bamboo invasion has contrasting effects on soil bacterial and fungal abundances, co-occurrence networks and their associations with enzyme activities in three broadleaved forests across subtropical China

Moso bamboo (Phyllostachys edulis) invasions into adjacent forests have been reported to threaten aboveground biodiversity and alter belowground soil processes. However, the impacts of bamboo invasion on soil microbial community composition, co-occurrence network and enzyme activity remain largely unknown. We presented a cross site field investigation on soil bacterial and fungal communities and enzyme activities in three forests (an original broadleaf forest, a mixed bamboo-broadleaf forest and a pure bamboo forest) at three sites in South China. Our results showed that bamboo invasion consistently increased soil pH (by 6.72% − 17.56%) and soil organic carbon concentrations (by 11.75% − 40.63%) across the three sites. Bamboo invasion consistently decreased fungal ITS gene abundances across the sites, but had little effect on bacterial 16S rRNA gene abundances and diversity indices. The community composition of both bacteria and fungi and their functional guilds differed among the three sites and were significantly (P < 0.05) affected by bamboo invasion. Bamboo invasion significantly decreased the relative abundances of ectomycorrhizal but increased those of soil saprotrophs. The complexity of co-occurrence network of bacterial communities was increased whereas that of fungal communities was decreased due to bamboo invasion. The activities of soil enzymes involved in C, N and P cycling were also altered by bamboo invasion, and they were significantly positively correlated with the abundances of fungal ITS gene and ectomycorrhizal rather than those of bacteria and predicted metabolic function. This study suggested that bamboo invasions into adjacent broadleaf forests had contrasting effects on soil bacterial and fungal communities by shifting microhabitats towards a condition that is unfavorable for some fungal functional guilds, which were tightly associated with soil functioning. These results highlight the need for sustainable forestry management against bamboo invasion to maintain fungal diversity and network complexity.

Microbial pathways account for the pH effect on soil N2O production

Clarifying the responses of different N2O production pathways to pH change is helpful to better understand the effect of pH on N2O emission from soils. A15N tracing study was carried out on subtropical forest (SF) and cropland (SC) soil in 30-day pH manipulation treatments to quantify the effect of pH on autotrophic nitrification, heterotrophic nitrification and denitrification-derived N2O. Gene abundances of autotrophic nitrification (AOA-amoA, AOB-amoA) and denitrification (nirK, nirS, nosZ) -related N2O production were determined to identify the microbial mechanism behind the pH effect on N2O production. The results showed that the total N2O production rate (N2Ot) of the SF soil was 4.56 and 4.86 μg N kg−1 day−1 at pH 3.5 and 4.5, respectively, which was significantly higher than the other treatments. Similarly, the highest N2Ot of the SC soil was also observed in pH 3.5 treatment (7.15 μg N kg−1 day−1). Both N2O production rate via denitrification (N2Od) and heterotrophic nitrification (N2Oh) markedly increased, while the N2O production rate via autotrophic nitrification (N2Oa) markedly decreased by decreasing pH in both the SF and SC soil. Thus, denitrification and heterotrophic nitrification were responsible for the high N2O production under strongly acidic conditions. The abundance of nosZ gene was significantly and negatively correlated with N2Od (P < 0.05), and the abundance of AOB-amoA was significantly and positively correlated with N2Oa (P < 0.01). The results of the structural equation modeling (SEM) analysis revealed that soil pH generated a more direct effect on the denitrifying and ammonia-oxidizing gene abundance, in turn, affected N2Od and N2Oa, respectively. In addition, soil pH exerted a significant effect on both the bacterial 16S rRNA and fungal ITS rDNA gene abundance (P < 0.05). However, the role of soil fungi and bacteria on N2Oh could not be determined in this study.

Effect of two contrasting biochars on soil microbiota in the humid tropics of Peninsular Malaysia

Report on soil microbial community in tropical soil of humid tropics remained limited despite the current research interest in biochar-microbe study in various climatic regions. A field-trial spanning three consecutive crop cycles of Zea mays var. Masmadu was conducted in tropical Acrisols of Peninsular Malaysia. Palm kernel shell and rice husk biochars of different feedstock and pyrolysis conditions were used for amendment. Soil samples were collected during maize harvesting and were analyzed for physicochemical properties (pH, CEC, organic C, labile active C), microbial biomass (C, N), and seven C-cycle enzymes activity (total cellulase, endoglucanase, β-glucosidase, xylanase, invertase, phenol oxidase, peroxidase). Total soil genomic DNA was extracted and subjected to the analysis of bacterial 16S rRNA and fungal ITS gene abundance quantification. Microbial genetic profiling was fingerprinted by using DGGE. Significant increases of all measured soil physicochemical properties, microbial biomass C, microbial biomass N, and gene abundances were observed in all biochar amended soils. Significant changes of total cellulase, endoglucanase, phenol oxidase, and peroxidase were not detected. A significant shift in microbial genotypic and enzymatic functional diversity based on microbial C-cycle enzymes was not detected. Correlation data revealed significant linkages of soil microbial biomasses and gene abundances with all measured soil physicochemical properties. The biochar influences the microbial community by elevating microbial habitat potential to a more favorable state and increasing labile active carbon sources in the field trial.

Spatial variability pattern of the anaerobic ammonia-oxidizing bacterial community across a salinity gradient from river to ocean

In natural habitats, the diversity of anaerobic ammonia-oxidizing (anammox) bacteria could be affected by multiple environmental variables. In this study, we investigated the distribution of the anammox bacterial community in surface sediment from the Dongjiang River (riverine sediment, DJ) to the Pearl River Estuary (estuarine sediment, PRE) and then to the South China Sea (coastal sediment, SCS). The results revealed evident differences in the structural diversity of anammox bacteria in three different habitats. Candidatus Brocadia accounted for approximately 90% of the total anammox bacteria in DJ, conversely, Ca. Scalindua dominated in the SCS. Nevertheless, Ca. Scalindua, Ca. Brocadia and Ca. Kuenenia coexisted in the PRE. The qPCR results indicated that anammox bacterial 16S rRNA gene abundance ranged from 2.23 × 105 to 1.19 × 107 copies g-1 of wet weight, but no significant correlation was found between the abundances and environmental variables (p > 0.05). The relative abundances of Ca. Brocadia gradually decreased with increasing salinity, and Ca. Scalindua showed the opposite trend, suggesting that salinity was a crucial factor in sculpturing the community composition of anammox bacteria in natural environments. Ca. Brocadia should be able to live in freshwater ecosystems, but it can also tolerate a certain level of salinity. Ca. Scalindua was halophilic anammox bacterium and exists only in saline environments. Ca. Kuenenia could adapt to a wide range of salinity and preferred to live in high DIN level conditions according to our search. The distribution pattern of anammox bacteria may be the result of microbial migration and long-term adaptation to salinity.

Abundance and community structure of ammonium monooxygenase (amoA) genes in the wet season of liaohe estuary sediments

Ammonia oxidation is an important part of the global nitrogen cycle. Ammonia-oxidizing archaea (AOA) and ammonia-oxidizing bacteria (AOB) are important players in the ammoxidation process. In this study, 13 sediment samples from the Liaohe estuary were collected in the wet season. The abundances of 16S rRNA and amoA genes were detected by real-time fluorescence quantitative PCR. The diversity and community structure of AOA and AOB were investigated by constructing clone libraries. The AOA and AOB amoA gene abundances ranged from 3.10 × 106–2.85 × 107 and 6.59 × 105–1.20 × 107 copies/g wet deposit, respectively. At all sites, AOA abundance was greater than AOB (AOA: AOB = 2.2–86.5). The ratio of AOA: archaeal 16S rRNA gene abundances and AOB: bacterial 16S rRNA gene abundances were 4.6 × 10−3–1.5 × 10−2 and 1.5 × 10−6–1.0 × 10−4. Phylogenetic analysis showed that the AOA amoA sequences were mainly Nitrosophaera and Nitrosopumilus, and most of the AOB amoA sequences belong to unclassified bacteria, which mainly were detected in estuarine sediments and wetland soils. AOA and AOB community had an obvious spatial heterogeneity. In addition, canonical correspondence analysis showed that the salinity, ammonia, total phosphorus, total organic carbon, sand, and silt content were the main driven factors of AOA and AOB community structure, in which the sand and silt content had a significant contribution.

Biochar-fertilizer interaction modifies N-sorption, enzyme activities and microbial functional abundance regulating nitrogen retention in rhizosphere soil

The impact of the excessive use of N fertilizer remains an environmental problem of global concern. The effect of biochar on soil N retention is still unclear, and knowledge on how a mixture of biochar and fertilizer (B-F) influence N-sorption, N-cycling enzymes activities, diversity and functional abundance of organisms regulating N-retention in rhizosphere soil is poorly understood. Therefore, biochars derived from bamboo, rice straw, cow and pig manure were characterized, and their interactions with NPK fertilizer were evaluated. Results showed that while the effect of biochar on N retention varied among biochar types, such variations increased after B-F. Unlike NH4+ retention, NO3− retention by biochar in fertilized soil was poor (<8 weeks), but were however increased after longer periods (15 weeks) in B-F due to plant uptake, sorption and stimulation of N-cycling enzymes activities. This stimulation proved that N-fertilizer provided substrates for N-cycling organisms which was confirmed by the dominance of Proteobacteria, Chloroflexi, Actinobacteria, and Gemmatimonadetes which are important in soil N-cycling, despite the reductions in total diversity, class, phyla and genera abundance of bacterial 16SrRNA genes by B-F. This suggested that B-F induced specific organisms involved in N-cycling, which out-competed other organisms not involved in N-cycling. The provision of substrates by N-fertilizer in B-F for bacterial groups involved in N-cycling modified the rhizosphere microbial structure. The abundance of N-cycling organisms was regulated by the persistence among dominant groups, soil pH, total N, and microbial colonization induced by different biochars interacting with fertilizer which led to enhanced N-retention.

Effects of straw and its biochar applications on the abundance and community structure of CO2-fixing bacteria in a sandy agricultural soil

Crop straw and biochar application can potentially increase carbon sequestration and lead to changes in the microbial community in agricultural soils. Sequestration of CO2 by autotrophic microorganisms is key to biogeochemical carbon cycling in soil ecosystems. The effects of straw and its biochar, derived from slow pyrolysis, on CO2 fixation bacteria in sandy soils, remain unclear. Therefore, this study compared the response of abundance and community of CO2 fixation bacteria to the two straw application methods in a sandy agricultural soil. The overall aim of the study was to achieve an efficient use of straw residues for the soil sustainablility. We investigated the soil organic carbon content and autotrophic bacteria over four consecutive years (2014–2018) in a field experiment, including the following four treatments: whole maize straw amendment (S), whole maize straw translated biochar amendment (B), half biochar and half straw amendment (BS), and control (CK) without straw or biochar amendment. The autotrophic bacterial abundance and community structure were measured using molecular methods of real-time PCR, terminal restriction fragment length polymorphisms (T-RFLP), and a clone library targeting the large subunit gene (cbbL) of ribulose-1,5-bisphosphate carboxylase/oxygenase. The results showed that the content of soil total organic carbon (TOC), dissolved organic carbon (DOC), and microbial biomass carbon (MBC) in B, S, and BS treatments was significantly increased compared with the CK treatment. Soil TOC and available potassium (AK) in the B treatment significantly increased by 15.4% and 23.3%, respectively, but soil bulk density, DOC, and MBC significantly decreased by 8.5%, 10.6%, and 14.5%, respectively, compared with the S treatment. The abundance of the cbbL gene as well as of the bacterial 16S rRNA gene increased significantly in straw or biochar application treatments as compared to the CK treatment. The B treatment, but not the BS treatment, significantly increased the cbbL gene abundance when compared to the S treatment. No significant differences were observed in the bacterial 16S rRNA gene abundance among the three straw or biochar applications. The application of straw biochar could increase the diversity of the autotrophic bacteria, which also altered the overall microbial composition. Physicochemical properties of the soil, such as soil pH, SOC, and bulk density, can help explain the shift in soil microbial composition observed in the study. Taken together, our results suggest that straw biochar, rather than straw application, leads to an increase in the abundance and diversity of CO2-fixing bacteria, which would be advantageous for soil autotrophic CO2 fixation.

Planktonic Bacterial and Archaeal Communities in an Artificially Irrigated Estuarine Wetland: Diversity, Distribution, and Responses to Environmental Parameters.

Bacterial and archaeal communities play important roles in wetland ecosystems. Although the microbial communities in the soils and sediments of wetlands have been studied extensively, the comprehensive distributions of planktonic bacterial and archaeal communities and their responses to environmental variables in wetlands remain poorly understood. The present study investigated the spatiotemporal characteristics of the bacterial and archaeal communities in the water of an artificially irrigated estuarine wetland of the Liaohe River, China, explored whether the wetland effluent changed the bacterial and archaeal communities in the Liaohe River, and evaluated the driving environmental factors. Within the study, 16S rRNA quantitative PCR methods and MiSeq high-throughput sequencing were used. The bacterial and archaeal 16S rRNA gene abundances showed significant temporal variation. Meanwhile, the bacterial and archaeal structures showed temporal but not spatial variation in the wetland and did not change in the Liaohe River after wetland drainage. Moreover, the bacterial communities tended to have higher diversity in the wetland water in summer and in the scarce zone, while a relatively higher diversity of archaeal communities was found in autumn and in the intensive zone. DO, pH and PO4-P were proven to be the essential environmental parameters shaping the planktonic bacterial and archaeal community structures in the Liaohe River estuarine wetland (LEW). The LEW had a high potential for methanogenesis, which could be reflected by the composition of the microbial communities.

Crop types have stronger effects on soil microbial communities and functionalities than biochar or fertilizer during two cycles of legume-cereal rotations of dry land.

The addition of biochar to agricultural fields has been widely studied, but most of these studies have emphasized its effects by growing a single type of crop over short- to long-term time spans. Additionally, a limited number of studies have focused on the soil microbial community composition with respect to biochar addition in legume-cereal crop rotation. In this study, we examined soil microbial community structures by adding biochar (0, 5, and 10tha-1) and fertilizer (nitrogen-N, phosphorous-P and potassium-K) during 2cycles of mash bean and wheat rotations. The results showed that the bacterial (16S rRNA) gene abundance was often increased by biochar addition in the presence of mash bean (Vigna mungo L.) but not wheat. When the soil received fertilizer, the bacterial gene abundance was less responsive to biochar addition. Fungal (ITS rRNA) copy numbers were enhanced by biochar and fertilizer in presence of wheat but were decreased in the presence of mash bean. Fertilizer addition also resulted in less change in ITS genes after biochar addition. Microbial functional groups including Gram+, Gram- and Pseudomonas bacteria were stimulated by biochar or fertilizer only in mash bean soils, while mycorrhizae were significantly increased by biochar in wheat soils. Although biochar addition affected soil properties, microbial community assays were not greatly altered by these physicochemical properties. In conclusion, the crop type played a decisive role, rather than biochar or fertilizer addition, in shaping microbial community structures (16S and ITS phyla) during crop rotation.

Impact of euxinic holomictic conditions on prokaryotic assemblages in a marine meromictic lake

The water column of marine Rogoznica Lake (Croatia) is stratified throughout the year. However, on rare occasions, the lake exhibits complete mixing, primarily driven by meteorological conditions. On such occasions, anoxic, sulfide-rich bottom water mixes with the oxic surface layer, triggering both the oxidation of sulfide predominantly to colloidal sulfur and the establishment of euxinic conditions throughout the water column. We investigated prokaryotic communities during euxinic holomictic conditions. High-throughput sequencing of the 16S rRNA gene showed that these sulfur-driven communities were dominated by Planctomycetales, chemolithotrophic Epsilonbactereota (mainly Arcobacteraceae) and Gammaproteobacteria (Thioglobaceae), followed by Alpha- (Rhodobacteraceae) and Deltaproteobacteria (Desulfobulbaceae and Desulfobacteraceae). The majority of archaeal sequences belonged to Nanoarchaeota, all of which were designated as Woesearchaeia. This class has not been recorded in other meromictic lakes. Both bacterial and archaeal 16S rRNA gene abundance did not vary significantly across the vertical profile of the lake, as shown by quantitative PCR. However, hierarchical clustering showed a significant difference between the microbial assemblage structure in stratified periods and during a holomictic event. Besides the structure, this stressful event had a manifold effect on bacterial and archaeal assemblages by decreasing their diversity and abundance when compared to the usual stratified conditions.

Assisted phytoremediation of a co-contaminated soil with biochar amendment: Contaminant removals and bacterial community properties

There are growing trends of combined contaminations in agricultural soils, and therefore it is urgently needed to remediate contaminated soils with eco-friendly approaches. This study aimed to evaluate the effects of Medicago sativa L. (alfalfa) planting, alone or together with biochar additions, on contaminant removals and bacterial properties in an agricultural soil contaminated by heavy metal and organic fungicide. The treatments in this study included: the control (CK), alfalfa planting (AP), alfalfa planting +1.5% biochar addition (w/w) (AP + 1.5B), alfalfa planting +3.0% biochar addition (AP + 3.0B), and alfalfa planting +6.0% biochar addition (AP + 6.0B). Relative to the alfalfa planting only, extra biochar additions increased alfalfa biomass and heavy metal cadmium (Cd) phytoextraction. The alfalfa planting, alone or together with biochar additions, significantly decreased soil iprodione concentrations. After 90 days of remediation, bacterial 16S rRNA gene abundances of the AP, AP + 1.5B, AP + 3.0B and AP + 6.0B treatments were 1.69, 3.84, 3.34 and 3.13 times as great as that obtained from the CK treatment, respectively. The AP + 1.5B treatment had the highest richness estimators and Shannon diversity index, but the AP + 6.0B treatment had the lowest invsimpson diversity index among the five treatments. The relative abundances of Bacteroidetes and Nitrospirae were enhanced by the alfalfa phytoremediation, alone or together with biochar additions. Our results suggest that the alfalfa has promising potentials in the remediation of co-contaminated soil and in the increases of soil bacterial biomass and community diversity. Simultaneously, biochar is beneficial to enhance Cd phytoextraction, however, biochar addition rate would need to be optimized.

Short-Term Response of the Soil Microbial Abundances and Enzyme Activities to Experimental Warming in a Boreal Peatland in Northeast China

Global warming is likely to influence the soil microorganisms and enzyme activity and alter the carbon and nitrogen balance of peatland ecosystems. To investigate the difference in sensitivities of carbon and nitrogen cycling microorganisms and enzyme activity to warming, we conducted three-year warming experiments in a boreal peatland. Our findings demonstrated that both mcrA and nirS gene abundance in shallow soil and deep soil exhibited insensitivity to warming, while shallow soil archaea 16S rRNA gene and amoA gene abundance in both shallow soil and deep soil increased under warming. Soil pmoA gene abundance of both layers, bacterial 16S rRNA gene abundance in shallow soil, and nirK gene abundance in deep soil decreased due to warming. The decreases of these gene abundances would be a result of losing labile substrates because of the competitive interactions between aboveground plants and underground soil microorganisms. Experimental warming inhibited β-glucosidase activity in two soil layers and invertase activity in deep soil, while it stimulated acid phosphatase activity in shallow soil. Both temperature and labile substrates regulate the responses of soil microbial abundances and enzyme activities to warming and affect the coupling relationships of carbon and nitrogen. This study provides a potential microbial mechanism controlling carbon and nitrogen cycling in peatland under climate warming.

Effects of Nitrogen and Phosphorus Inputs on Soil Bacterial Abundance, Diversity, and Community Composition in Chinese Fir Plantations.

Nutrient inputs to forest ecosystems significantly influence aboveground plant community structure and ecosystem functioning. However, our knowledge of the influence of nitrogen (N) and/or phosphorus (P) inputs on belowground microbial communities in subtropical forests is still unclear. In this study, we used quantitative polymerase chain reaction and Illumina Miseq sequencing of the bacterial 16S rRNA gene to investigate bacterial abundance, diversity, and community composition in a Chinese fir plantation. The fertilization regimes were as follows: untreated control (CK), P amendment (P), N amendment (N), and N with P amendment (NP). Additions of N decreased soil pH and bacterial 16S rRNA gene abundance by 3.95 (from 4.69 to 3.95) and 3.95 × 109 copies g−1 dry soil (from 9.27 × 109 to 3.95 × 109 g−1 dry soil), respectively. Bacterial richness and diversity decreased with N addition (N and NP) rather than only P input. Proteobacteria, Acidobacteria, and Actinobacteria were the major phylum across all treatments. Nitrogen addition increased the relative abundance of Proteobacteria and Actinobacteria by 42.0 and 10.5%, respectively, while it reduced that of Acidobacteria by 26.5%. Bacterial community structure in the CK and P treatments was different from that in the N and NP treatments upon principle coordinates analysis. Phosphorus addition did not significantly affect soil bacterial communities, and no interactions between N and P inputs on microbial traits were observed. Soil pH and mineral N availability appeared to have a cooperative effect on bacterial abundance and community structure, with soil pH being the key influencing factor by canonical correspondence analysis. These results indicate that inorganic N rather than P fertilization affected both bacterial abundance and community composition in subtropical forests.

Impacts of long-term nitrogen addition, watering and mowing on ammonia oxidizers, denitrifiers and plant communities in a temperate steppe

Global changes in nitrogen (N) deposition, precipitation patterns and land use could have an impact on the biogeochemical N cycle mediated by microorganisms. Microbial responses to global changes have been generally evaluated in short-term studies, while the long-term effects are not well understood. In this study, the interactive effects of multiple global change factors on N-cycling microorganisms and their interactions with plants were investigated in a 9-year field experiment with N addition, watering and mowing in a temperate steppe in northern China. Quantitative PCR, terminal restriction fragment length polymorphism (T-RFLP) and clone library were used to analyze the abundance and community structure of ammonia oxidizers and denitrifiers, respectively. Bacterial 16S rRNA gene abundance significantly increased under mowing, but the functional gene abundances including amoA, nirS, nirK and nosZ genes were not affected. Watering significantly affected the ammonia-oxidizing archaea (AOA) community and N addition showed a strong effect on soil ammonia-oxidizing bacteria (AOB) and nosZ-containing denitrifier community structure. No significant interactive effects of mowing, N addition and watering on communities of soil ammonia oxidizers and denitrifiers were observed. Structure equation models suggested that plant biomass and community were significantly correlated with microbial communities and activities. These findings suggest that there are complex interactions between plants and soil microorganisms in grassland ecosystems.

Revitalisation of metal-contaminated, EDTA-washed soil by addition of unpolluted soil, compost and biochar: Effects on soil enzyme activity, microbial community composition and abundance

Soil remediation mitigates hazards from contaminants but could deprive soils of initial biota and enzymes. Historically contaminated acidic soil from Arnoldstein (Austria) and calcareous soil from Meza (Slovenia) were washed with 30 and 100 mmol kg−1 ethylenediaminetetraacetate (EDTA) to remove 78 and 60% of Pb as a main pollutant. Remediation of the Arnoldstein soil decreased urease activity and increased β-glucosidase activity, measured in a 15-week experiment. The dehydrogenase activity and microbial gene abundances were not significantly impeded compared to the original soil. Conversely, the use of a high dose of EDTA in the Meza soil, necessary for effective remediation of calcareous soils, resulted in pronouncedly decreased enzyme activities (3.2 times on average) and repressed fungal ITS and increased bacterial 16S rRNA gene abundance. Remediation shifted the microbial community composition in both soils. For revitalisation, the remediated soils were amended with compost, inocula of un-contaminated soil and (Arnoldstein soil) biochar enriched with soil extract. Amendments inconsistently affected the Arnoldstein soil: compost increased the dehydrogenase activity and altered the microbial community composition, biochar enhanced the β-glucosidase activity, and all amendments decreased the microbial abundance (1.6 times on average). In contrast, amendments efficiently revitalised the remediated Meza soil; compost and soil inoculum returned the enzyme activities back to the baseline in the original soil, increased the fungal abundance above that in the original soil and restored the microbial community composition.