RESUMEN

Water reservoir sediments represent a distinct habitat that harbors diverse microbial resources crucial for nitrogen cycling processes. The discovery of resuscitation promoting factor (Rpf) has been recognized as a crucial development in understanding the potential of microbial populations. However, our understanding of the relationship between microorganisms containing rpf-like genes and nitrogen-cycling functional populations remains limited. The present study explored the distribution patterns of rpf-like genes and nitrogen-cycling genes in various water reservoir sediments, along with their correlation with environmental factors. Additionally, the co-occurrence of rpf-like genes with genes associated with the nitrogen cycle and viable but non-culturable (VBNC) formation was investigated. The findings indicated the ubiquitous occurrence of Rpf-like domains and their related genes in the examined reservoir sediments. Notably, rpf-like genes were predominantly associated with Bradyrhizobium, Nitrospira, and Anaeromyxobacter, with pH emerging as the primary influencing factor for their distribution. Genera such as Nitrospira, Bradyrhizobium, Anaeromyxobacter, and Dechloromonas harbor the majority of nitrogen-cycling functional genes, particularly denitrification genes. The distribution of nitrogen-cycling microbial communities in the reservoir sediments was mainly influenced by pH and NH4 +. Notably, correlation network analysis revealed close connections between microorganisms containing rpf-like genes and nitrogen-cycling functional populations, as well as VBNC bacteria. These findings offer new insights into the prevalence of rpf-like genes in the water reservoir sediments and their correlation with nitrogen-cycling microbial communities, enhancing our understanding of the significant potential of microbial nitrogen cycling.

RESUMEN

Quantification of nitrogen (N) cycling genes contributes to our best understanding of N transformation processes. The application of organic amendment (OA) is widely recognized as an effective measure to improve N management and soil fertility in various ecosystems. However, our understanding of N-cycling gene abundances in response to OA application remains deficient. We performed a meta-analysis embracing 124 sets of observation data to study the impact of OA application on the main N-cycling gene abundances, including nifH, amoA, nirS, nirK and nosZ. We found that the significantly positive response of N-cycling gene abundances to OA application was attributed to the rotation cropping system (by 6.45 %-104.20 %) in the field experiment (by 19.43 %-52.56 %), OA application alone (by 8.29 %-111.70 %) especially manure addition (by 33.43 %-98.70 %), application dose of OAs within 10-20 t ha-1 (by 45.33 %-381.90 %), fertilization duration <5 years (by 43.69 %-112.63 %), C/N of OA <25 (by 37.87 %-160.90 %), SOC lower than 1.2 % (by 41.44 %-157.89 %) and application to alkaline soil (by 32.24 %-134.40 %). Moreover, soil organic carbon (SOC) and pH were the most essential regulators associated with N-cycling gene abundances with OA application. Identification of key driving factors of the abundance of N-cycling functional genes will help remedy strategies for managing OAs in ecosystems.

Asunto(s)

RESUMEN

Intensive aquaculture in high-density hybrid snakehead [Channa maculata (♀) × Channa argus (♂)] fishponds can lead to toxic conditions for fish. This study investigated nitrogen migration and transformation in these fishponds during different cultivation periods. Using qPCR technology, we analyzed the abundance variation of nitrogen-cycling microorganisms in water and sediment to reveal the nitrogen metabolism characteristics of hybrid snakehead fishponds. The results showed that fish biomass significantly impacts suspended particulate matter (SPM) flux. At the sediment-water interface, inorganic nitrogen fluxes showed predominant NO3--N absorption by sediments and NH4+-N and NO2--N release, especially in later cultivation stages. Sediments were rich in nirS and AMX 16S rRNA genes (ranging from 4.04 × 109 to 1.01 × 1010 and 1.19 × 108 to 2.62 × 108 copies/g, respectively) with nirS-type denitrifiers potentially dominating the denitrification process. Ammonia-oxidizing bacteria (AOB) were found to dominate the ammonia oxidation process over ammonia-oxidizing archaea (AOA) in both water and sediment. Redundancy analysis revealed a positive correlation between SPM flux, Chlorophyll a (Chl-a), and denitrification genes in the water, and between nitrogen-cycling genes and NH4+/NO2- fluxes at the interface. These findings provide a scientific basis for nitrogen control in hybrid snakehead fishponds.

RESUMEN

The structure and function of the water microbial community can change dramatically between different rearing modes. Yet investigations into the relationships between microbial community and water quality remain obscure. We provide the first evidence that rearing modes alter bacterial community and water quality in the rearing water of the mud crab (Scylla paramamosain) larvae. The juveniles in the recirculating aquaculture system (RAS) had a higher viability than those in the water exchange system (WES). RAS had the significantly lower levels of total ammonia nitrogen (TAN), NH3, NO2--N, total nitrogen (TN), total dissolved solids (TDS), and chemical oxygen demand than those of WES. The number of significantly different amplicon sequence variants between rearing modes increased as the larvae developed. NH3, TAN, TDS, NO2--N, and TN were closely related to the late alterations in water bacterial community. Both the FAPROTAX tool and quantitative PCR analysis showed enhanced nitrogen cycling functional potential of water bacterial community of RAS. Random forest analysis identified the enriched water bacteria especially heterotrophic bacteria such as Phaeodactylibacter, Tenacibaculum, and Hydrogenophaga, which were vital in removing nitrogenous compounds via simultaneous nitrification and denitrification. Notably, RAS could save 18.5 m3 of seawater relative to WES in larviculture on the scale of 2.5 m3. Together, these data indicate that RAS could function as microbial community and water quality management strategy in the larviculture of crab.

Asunto(s)

RESUMEN

Antarctic deserts, such as the McMurdo Dry Valleys (MDV), represent extremely cold and dry environments. Consequently, MDV are suitable for studying the environment limits on the cycling of key elements that are necessary for life, like nitrogen. The spatial distribution and biogeochemical drivers of nitrogen-cycling pathways remain elusive in the Antarctic deserts because most studies focus on specific nitrogen-cycling genes and/or organisms. In this study, we analyzed metagenome and relevant environmental data of 32 MDV soils to generate a complete picture of the nitrogen-cycling potential in MDV microbial communities and advance our knowledge of the complexity and distribution of nitrogen biogeochemistry in these harsh environments. We found evidence of nitrogen-cycling genes potentially capable of fully oxidizing and reducing molecular nitrogen, despite the inhospitable conditions of MDV. Strong positive correlations were identified between genes involved in nitrogen cycling. Clear relationships between nitrogen-cycling pathways and environmental parameters also indicate abiotic and biotic variables, like pH, water availability, and biological complexity that collectively impose limits on the distribution of nitrogen-cycling genes. Accordingly, the spatial distribution of nitrogen-cycling genes was more concentrated near the lakes and glaciers. Association rules revealed non-linear correlations between complex combinations of environmental variables and nitrogen-cycling genes. Association rules for the presence of denitrification genes presented a distinct combination of environmental variables from the remaining nitrogen-cycling genes. This study contributes to an integrative picture of the nitrogen-cycling potential in MDV.

RESUMEN

In this study, we set up a soil-microbe-soybean system spiked with PFOA, PFOS, or a PFAS mixture of eight PFAS and investigated the distribution of PFAS in the system and impacts on the abundance and expression level of genes involved in the nitrogen (N) cycle. When soybean was exposed to the PFAS mixtures, synergistic uptake by shoots was detected. PFAS exhibited remarkable impacts on abundance of nitrification and denitrification genes in both bulk soil and rhizosphere as well as expression of N fixation gene in soybean nodules. The abundance of nitrification genes AOA and AOB amoA and denitrification gene nirK was significantly reduced (p < 0.05) in almost all treatments in bulk soil, except PFOA at 10 µg/kg. The abundance of other functional genes, such as nirS and norZ was affected differently depending on PFAS concentrations and sample location, either bulk soil or the rhizosphere. Interestingly, the N fixation gene nifH in soybean nodules was overexpressed by a PFAS mixture at 100 µg/kg. Hence, this work provided in-depth knowledge regarding the distribution of PFAS and their impacts on the N cycle for the studied system. Results from this study provide insights on assessing risks posed by individual or mixed PFAS to soybean.

Asunto(s)

RESUMEN

Desert wetlands are evolving into deserts by groundwater table (GWT) drawdown. However, the changes in microbial communities and functions during the GWT drawdown are unclear, which hinders the predictive power of biogeochemical processes across the desertification. Here, 16S rRNA gene sequencing, PICRUSt2 and qPCR were used to investigate soil prokaryotic diversity, composition and nitrogen cycling gene abundance at four vegetation types [flooded swamp (FS), drained swamp (DS), desert grassland (DG), and bare sandy land (BS)] along a GWT decline gradient in the Mu Us Desert, northern China. Results showed that prokaryotic Shannon and Chao1 indexes were significantly reduced at BS than those at FS (p < 0.05). Whereas no significant difference was observed between FS, DS and DG (p > 0.05). Distinct shifts in community composition were found along the GWT decline gradient. The dominant taxa gradually changed from obligate anaerobes and eutrophic microbes to facultative anaerobes, and finally to aerobic, oligotrophic and drought-tolerant microbes. Soil moisture was the most important factor in regulating the communities. In addition, GWT drawdown inhibited the relative abundance of genes involved in nitrogen fixation, assimilatory nitrite reduction, and nitrate oxidation, but enhanced the relative abundance of genes related to denitrification, assimilated nitrate reduction, ammonia oxidation and ammonification. Thus, GWT drawdown inhibits nitrogen input potential and exacerbates nitrogen loss potential. These results help in understanding the succession characteristics of desert wetland desertification.

Asunto(s)

RESUMEN

Apart from chemical constituents, wastewater treatment plant (WWTP) effluents also release microorganisms that can be important to the receiving water bodies either from a sanitary point of view, or taking to the account the biogeochemical potential of the recipients. However, little is known about the treated wastewater microbial community, its composition, seasonal changes, functions and fate in the waters of the receiver. Thus, this study presents a synergistic approach coupling new and traditional methods: analytical chemistry, classical microbiology (cultivation- and microscopy-based methods), as well as Next Generation Sequencing and a quantitative real-time polymerase chain reaction (qPCR). The results show that in terms of bacterial community composition, treated wastewater differed from the environmental samples, irrespectively if they were related or unrelated to the WWTP effluent discharge. The canonical correspondence analysis (CCA) taking into account chemical parameters and taxonomical biodiversity indirectly confirmed the seasonal deterioration of the treated wastewater quality as a result of temperature-driven change of activated sludge community structure and biomass washout (observed also by DAPI staining). Despite seasonal fluctuations of total suspended solids and inter-related parameters (such as COD, BOD, TN, TP), the treated wastewater quality remained within current discharge limits. It was due to treatment processes intensively adjusted by WWTP operators, particularly those necessary to maintain an appropriate rate of autotrophic processes of nitrification and to support biological phosphorus removal. This can explain the observed microbiome composition similarity among WWTP effluents at high taxonomic levels. Obtained data also suggest that besides wastewater treatment efficiency, WWTP effluents are still sources of both human-related microorganisms as well as bacteria equipped in genes involved in N-cycling. Their potential of participation in nutrients cycling in the receivers is widely unknown and require critical attention and better understanding.

Asunto(s)

RESUMEN

Cadmium (Cd) is the most concerning soil pollutant, and a threat to human health, especially in China. The in-situ immobilization of Cadmium by amendments is one of the most widely adopted methods to remedy soil contamination. The study was designed to evaluate the effect of organo-chemical amendments on soil Cd bioavailability and nitrogen cycling microbes under continuous planting of rice (Oryza sativa) and pak choi (Brassica chinensis L.). The experiment was carried out using four amendments, Lime, Zeolite, Superphosphate, and Biochar, at two different ratios; M1: at the ratio of 47:47:5:1, and M2 at the ratio of 71:23:5:1, respectively. Moreover, both M1 and M2 were enriched at four levels (T1: 0.5%; T2: 1%; T3: 2%; T4: 4%). Results showed that compared with CK (Cd enriched soils), the yield of rice under treatments of M1T1 and M2T1 increased by 8.93% and 8.36%, respectively. While the biomass (fresh weight) of pak choi under M1 and M2 amendments increased by 2.52-2.98 times and 0.76-2.89 times respectively, under enrichment treatments T1, T2, and T3. The total Cd concentrations in rice grains treated with M1T3 and M2T3 decreased by 89.25% and 93.16%, respectively, compared with CK. On the other hand, the total Cd concentrations in pak choi under M1T3 and M2T2 decreased by 92.86% and 90.23%, respectively. The results showed that soil pH was the main factor affecting Cd bioavailability in rice and pak choi. The Variance partitioning analysis (VPA) of rice and pak choi showed that soil pH was the most significant contributing factor. In the rice season, the contribution of soil pH (P) on Cd bioavailability was 10.14% (P = 0.102), and in the pak choi season, the contribution of soil pH was 8.38% (P = 0.133). Furthermore, the abundance of ammonia oxidation and denitrifying microorganisms had significantly correlation with soil pH and exchange Cd. In rice season, when the enrichment level of amendments increased from 0.5% (T1) to 2% (T3), the gene abundance of AOA, AOB, nirK, nirS and nosZ (І) tended to decrease. While in pak choi season, when the enrichment level increased at the level of 0.5% (T1), 1% (T2), and 2% (T3), the gene abundance of AOB, nirS, and nosZ (І) increased. Additionally, the gene abundance of AOA and nirK showed a reduction in the pak choi season contrasting to rice. And the mixed amendment M2 performed better at reducing Cd uptake than M1, which may have correlation with the ratio of lime and zeolite in them. Finally, we conclude that between these two amendments, when applied at a moderate level M2 type performed better than M1 in reducing Cd uptake, and also showed positive effects on both gene abundance and increase soil pH.

Asunto(s)

RESUMEN

Understanding interspecies interactions is essential to predict the response of microbial communities to exogenous perturbation. Herein, rhizospheric and bulk soils were collected from five developmental stages of soybean, which grew in soils receiving 16-year nitrogen inputs. Bacterial communities and functional profiles were examined using high-throughput sequencing and quantitative PCR, respectively. The objective of this study was to identify the key bacterial interactions that influenced community dynamics and functions. We found that the stages of soybean development outcompeted nitrogen fertilization management in shaping bacterial community structure, while fertilization treatments significantly shaped the abundance distribution of nitrogen functional genes. Temporal variations in bacterial abundances increased in bulk soils, especially at the stage of soybean branching, which helps to infer underlying negative interspecies interactions. Members of Cyanobacteria and Actinobacteria actively engaged in inter-phylum negative interactions in bulk soils and soybean rhizosphere, respectively. Furthermore, the negative interactions between nitrogen-fixing functional groups and the reduction of nifH gene abundance were coupled during soybean development, which may help to explain the linkages between population dynamics and functions. Overall, these findings highlight the importance of inter-phylum negative interactions in shaping the correlation patterns of bacterial communities and in determining soil functional potential.

RESUMEN

Currently, wastewater treatment plant (WWTP) upgrades have been implemented in various countries to improve the water quality of the receiving ecosystems and protect aquatic species from potential deleterious effects. The impact of WWTP upgrades on biological communities and functions in receiving waters is a fundamental issue that remains largely unaddressed, especially for microbial communities. Here, we selected two wastewater-dominant rivers in Beijing (China) as study sites, i.e., one river receiving water from an upgraded WWTP to explore the impacts of upgrade on aquatic ecosystems and another river receiving water from a previously upgraded WWTP as a reference. After a five-year investigation, we found that WWTP upgrade significantly decreased total organic nitrogen (N) in the receiving river. As a biological response, N-metabolism-related bacterioplankton are accordingly altered in composition and tend to intensively interact according to the network analysis. Metagenomic analysis based on the N-cycling genes and metagenomic-assembled genomes revealed that WWTP upgrade decreased the abundance of nitrifying bacteria but increased that of denitrifying and dissimilatory nitrate reduction to ammonium (DNRA) bacteria in the receiving river, according to their marker gene abundances. After calculation of the ratios between DNRA and denitrifying bacteria and quantification of genes/bacteria related to ammonium cycling, we deduced the changes in N-metabolism-related bacteria are likely an attempt to provide enough bioavailable N for plankton growth as conservation of ammonium was enhanced in receiving river after WWTP upgrade.

Asunto(s)

RESUMEN

This study investigated the effects of long-term soil fertilization on the composition and potential for phosphorus (P) and nitrogen (N) cycling of bacterial communities associated with hyphae of the P-solubilizing fungus Penicillium canescens Using a baiting approach, hyphosphere bacterial communities were recovered from three soils that had received long-term amendment in the field with mineral or mineral plus organic fertilizers. P. canescens hyphae recruited bacterial communities with a decreased diversity and an increased abundance of Proteobacteria relative to what was observed in soil communities. As core bacterial taxa, Delftia and Pseudomonas spp. were present in all hyphosphere samples irrespective of soil fertilization. However, the type of fertilization showed significant impacts on the diversity, composition, and distinctive taxa/operational taxonomic units (OTUs) of hyphosphere communities. The soil factors P (Olsen method), exchangeable Mg, exchangeable K, and pH were important for shaping soil and hyphosphere bacterial community compositions. An increased relative abundance of organic P metabolism genes was found in hyphosphere communities from soil that had not received P fertilizers, which could indicate P limitation near the fungal hyphae. Additionally, P. canescens hyphae recruited bacterial communities with a higher abundance of N fixation genes than found in soil communities, which might imply a role of hyphosphere communities for fungal N nutrition. Furthermore, the relative abundances of denitrification genes were greater in several hyphosphere communities, indicating an at least partly anoxic microenvironment with a high carbon-to-N ratio around the hyphae. In conclusion, soil fertilization legacy shapes P. canescens hyphosphere microbiomes and their functional potential related to P and N cycling.IMPORTANCE P-solubilizing Penicillium strains are introduced as biofertilizers to agricultural soils to improve plant P nutrition. Currently, little is known about the ecology of these biofertilizers, including their interactions with other soil microorganisms. This study shows that communities dominated by Betaproteobacteria and Gammaproteobacteria colonize P. canescens hyphae in soil and that the compositions of these communities depend on the soil conditions. The potential of these communities for N and organic P cycling is generally higher than that of soil communities. The high potential for organic P metabolism might complement the ability of the fungus to solubilize inorganic P, and it points to the hyphosphere as a hot spot for P metabolism. Furthermore, the high potential for N fixation could indicate that P. canescens recruits bacteria that are able to improve its N nutrition. Hence, this community study identifies functional groups relevant for the future optimization of next-generation biofertilizer consortia for applications in soil.

Asunto(s)

RESUMEN

The Yellow River Delta (YRD) region is an important production base in Shandong Province. It encompasses an array of diversified crop systems, including the corn-wheat rotation system (Wheat-Corn), soybean-corn rotation system (Soybean-Corn), fruits or vegetables system (Fruit), cotton system (Cotton) and rice system (Rice). In this study, the communities of ammonia oxidizer-, denitrifier- and nitrogen (N)-fixing bacteria in those cropping systems were investigated by Illumina Miseq sequencing. We found that Rice soil exhibited significantly higher diversity indices of investigated N-cycling microbial communities than other crop soils, possibly due to its high soil water content. Wheat-Corn soils had higher abundances of nitrification gene amoA and denitrification genes nirK and nirS, and exhibited higher soil potential nitrification rate (PNR), compared with Soybean-Corn, Cotton and Fruit soils. Consistently, redundancy analysis (RDA) showed that soil water content (SWC), electrical conductivity (EC), and total nitrogen (TN) were the most important influencing factors of the diversity and structure of the investigated N-cycling microbial.

RESUMEN

The objective of this study was to identify the effect of clay additive to explore the nitrogen cycling related ammonification, denitrifying genes and their relation N2O and ammonia emission during the chicken manure (CM) composting. The consequences indicated that the additive clay could optimize the environment and improve the NH4+-N into NO3--N transformation. Meanwhile, the results observed that 8% clay amendment was significant correlated the abundance of nifH and nosZ genes. Compared with the other treatments, the 6% and 10% clay treatments observed low abundance of nifH. The heat map indicated that clay amendment could enhance the function genes abundance. The redundancy analysis showed that N2O and ammonia emission among all physiochemical parameters had great relationship with functional genes. Therefore, the addition of 10% clay into CM composting system could efficiently enhance the abundance of nirK and narG genes, and improve the composting with its application.

Asunto(s)

RESUMEN

Tetrabromobisphenol A (TBBPA) and copper (Cu) are the main pollutants at e-waste recycling sites and the effects of their biotoxicity on microorganisms have drawn extensive attention. Nitrate-based bioremediation has been applied to organic pollutant-contaminated sediments since nitrate is a favorable electron acceptor for microbes. However, the effects of TBBPA and Cu on nitrogen (N)-cycling microorganisms and bioremediation in co-contaminated sediments remain unclear. Thus, our study examined the effects of TBBPA and Cu with/without nitrate addition on the TBBPA biodegradation efficiencies, microbial activities, and N functional genes. It was found the biodegradation efficiencies of TBBPA were improved by the nitrate addition from 34.7% to 59.3% and from 22.6% to 42.8% in the TBBPA and TBBPA-Cu contaminated groups, respectively. The inhibitions of the catalase activity increased with the nitrate addition because of the anaerobic respiration of the microorganisms. In addition, the potential denitrification rate exhibited an increasing trend from 6.46 to 8.23 mg-N kg-1 dry sediment day-1 during the period of 15-90 days after adding nitrate to the co-contaminated group, whereas the potential nitrification rate exhibited an opposite trend and decreased from 4.47 to 3.19 mg-N kg-1 dry sediment day-1. The denitrification gene abundances of the N-cycling genes were 107-108 orders of magnitude higher and significantly increased in the nitrate addition groups. The amoA gene abundances were lower than the denitrification gene abundances and were 105-106 orders of magnitude in the same groups. Moreover, the interaction types of the pollutants on the gene abundances were changed from synergistic to antagonistic as nitrate addition. Our study emphasized the gap of knowledge on nitrate addition affecting N-cycling microbes in the combined pollutants exposure sediments, and will be helpful for further bioremediation in different contaminated scenarios.

Asunto(s)

RESUMEN

Biofilms mediate crucial biochemical processes in aquatic ecosystems. It was hypothesized that eutrophication may promote the growth of biofilms, resulting in larger numbers of functional genes. However, the metabolic activity and the roles of biofilms in N cycling will be affected by ambient inorganic nitrogen availability, not by the abundance of functional genes. Biofilms were cultured either with replete inorganic nitrogen (N-rep) or without exogenous inorganic nitrogen supply (N-def) in a flow incubator, and the N-cycling gene abundances (nifH, N2 fixation; amoA, ammonia oxidation, archaea and bacteria; nirS and nirK, denitrification) and enzyme activities (nitrogenase and nitrate reductase) were analyzed. The results showed that, comparing the N-def and N-rep biofilms, the former contained lower nifH gene abundance, but higher nitrogenase activity (NA), while the latter contained higher nifH gene abundance, but lower NA. Different patterns of NA diel variations corresponded to the dynamic microbial community composition and different stages of biofilm colonization. Ammonia oxidizing bacteria (AOB), detected only in N-def biofilms, were responsible for nitrification in biofilms. N-rep biofilms contained high nirS and nirK gene abundance and high denitrification enzyme activity, but N-def biofilms contained significantly lower denitrification gene abundance and activity. In general, the strong N2 fixation in N-def biofilms and strong denitrification in N-rep biofilms assured the balance of aquatic ecosystems. The results suggested that evaluation of the functional processes of N cycling should not only focus on genetic potential, but also on the physiological activity of biofilms.

Asunto(s)

RESUMEN

BACKGROUND AND AIMS: Soil degradation is a major global problem; to investigate the potential for recovery of soil biota and associated key functions, soils were monitored during the early years of conversion between permanent grassland, arable cropping and bare fallow (maintained by regular tilling). Distinct differences in soil properties had become apparent 50 years after a previous conversion. METHODS: Subplots on previously permanent grassland, arable and bare fallow soil were converted to the two alternatives, generating 9 treatments. Soil properties (soil organic carbon, mesofauna, microbial community structure and activity) were measured. RESULTS: After 2 years, mesofauna and microbial abundance increased where plants were grown on previously bare fallow soils and declined where grassland was converted to bare fallow treatment. Overall prokaryote community composition remained more similar to the previous treatments of the converted plots than to the new treatments but there were significant changes in the relative abundance of some groups and functional genes. Four years after conversion, SOC in arable and bare fallow soils converted to grassland had increased significantly. CONCLUSIONS: Conversion to permanent grassland effectively replenished C in previously degraded soil; the soil microbiome showed significant conversion-related changes; plant-driven recovery was quicker than C loss in the absence of plants.