Microorganisms mediate nutrient cycling in soils, and thus it is assumed that they largely control responses of terrestrial ecosystems to anthropogenic nutrient inputs. Therefore, it is important to ...understand how increased nitrogen (N) and phosphorus (P) availabilities, first, affect soil prokaryotic and fungal community composition and second, if and how changes in the community composition affect soil element cycling. We measured soil microbial communities and soil element cycling processes along a nine-year old experimental N-addition gradient partially crossed with a P-addition treatment in a temperate grassland. Nitrogen addition affected microbial community composition, and prokaryotic communities were less sensitive to N addition than fungal communities. P addition only marginally affected microbial community composition, indicating that P is less selective than N for microbial taxa in this grassland. Soil pH and total organic carbon (C) concentration were the main factors associated with prokaryotic community composition, while the dissolved organic C-to-dissolved N ratio was the predominant driver of fungal community composition. Against our expectation, plant biomass and plant community structure only explained a small proportion of the microbial community composition. Although microbial community composition changed with nutrient addition, microbial biomass concentrations and respiration rates did not change, indicating functional redundancy of the microbial community. Microbial respiration, net N mineralization, and non-symbiotic N2 fixation were more strongly controlled by abiotic factors than by plant biomass, plant community structure or microbial community, showing that community shifts under increasing nutrient inputs may not necessarily be reflected in element cycling rates. This study suggests that atmospheric N deposition may impact the composition of fungi more than of prokaryotes and that nutrient inputs act directly on element-cycling rates as opposed to being mediated through shifts in plant or microbial community composition.
Display omitted
•Nutrient inputs differentially impacted microbial communities and element cycling.•Soil pH and total organic carbon were main drivers of prokaryotic communities.•DOC:DN ratio was the predominant driver of fungal community composition.•Element cycling was controlled by abiotic factors, not by microbial community change.•Microbial community change may not necessarily change ecosystem functioning.
About 1.3 billion tons of food waste (FW) is annually produced at a global scale. A major fraction of FW is deposited into landfills thereby contributing to environmental pollution and emission of ...greenhouse gasses. While increasing amounts of FW are recycled more sustainably into fertilizers in industrial-scale composting, very little is known about the antibiotic resistance genes (ARGs) present in FW and how their abundance is affected by composting. To study this, we quantified the diversity and abundance of ARGs, mobile genetic elements (MGEs) and bacterial communities in the beginning, during and at the end of the FW composting. All targeted 27 ARGs and 5 MGEs were detected in every sample suggesting that composted FW remains a reservoir of ARGs and MGEs. While the composting drastically changed the abundance, composition and diversity of bacterial communities, an increase in total ARG and MGE abundances was observed. Changes in ARGs were linked with shifts in the composition of bacterial communities as revealed by a Procrustes analysis (P < 0.01). Crucially, even though the high composting temperatures reduced the abundance and diversity of initially ARG-associated bacterial taxa, ARG abundances were maintained in other associated bacterial taxa. This was likely driven by horizontal gene transfer and physicochemical composting properties as revealed by a clear positive correlation between ARGs, MGEs, pH, NO3− and moisture. Together our findings suggest that traditional composting is not efficient at removing ARGs and MGEs from FW. More effective composting strategies are thus needed to minimize ARG release from composted FW into agricultural environments.
Display omitted
•Food waste is an important reservoir of ARGs and MGEs.•The composition of potential ARGs carrier changed during FW composting.•Composting properties are vital drivers to affecting the abundances of ARGs.•Shifts in bacterial community composition are associated with the maintenance of ARGs.
Heavy metal pollution caused by mining activities can be harmful to soil microbiota, which are highly sensitive to heavy metal stress. This study aimed to investigate the response of soil bacterial ...communities to varying levels of heavy metal pollution in four types of habitats (i.e., tailing, remediation, natural recovery, and undisturbed areas) at an abandoned polymetallic mine by high-throughput 16 S rRNA gene sequencing, and to determine the dominant ecological processes and major factors driving the variations in bacterial community composition. The diversity and composition of bacterial communities varied significantly between soil habitats (p < 0.05). Heterogeneous selection played a crucial role in shaping the difference of bacterial community composition between distinct soil habitats. Redundancy analysis and Pearson correlation analysis revealed that the total contents of Cu and Zn were key factors causing the difference in bacterial community composition in the tailing and remediation areas, whereas bioavailable Mn and Cd, total nitrogen, available nitrogen, soil organic carbon, vegetation coverage, and plant diversity were key factors shaping the soil bacterial structure in the undisturbed and natural recovery areas. These findings provide insights into the distribution patterns of bacterial communities in soil habitats with different levels of heavy metal pollution, and the dominant ecological processes and the corresponding environmental drivers, and expand knowledge in bacterial assembly mechanisms in mining regions.
Display omitted
•Soil bacterial composition was significantly different between four types of habitats.•Soil bacterial diversity in tailing area was lowest, but highest in undisturbed area.•Heterogeneous selection governed the bacterial distribution across distinct areas.•Cu and Zn primarily shaped bacterial composition in tailing and remediation areas.•Soil nutrients and vegetation were key for natural recovery and undisturbed areas.
Increased nitrogen (N) deposition endangers the biodiversity and stability of forest ecosystems, and much of the original phosphorus (P) parent material continues to decrease in most lowland tropical ...forests. It remains poorly understood as to how soil microbial diversity at a molecular level responds to the addition of excess N and mitigation of soil P limitation, as well as their influencing factors, in the N-rich tropical forest ecosystems. To reach a better understanding, we conducted a six-year N and P-addition experiment consisting of three treatments: N-addition (150 kg N ha−1 yr−1), P-addition (150 kg P ha−1 yr−1), and NP-addition (150 kg N ha−1 yr−1 plus 150 kg P ha−1 yr−1), besides a control treatment in an old-growth tropical forest in southern China. We examined the snapshot responses of soil bacterial richness and community composition to the elevated N and P levels after six years using a 16S rRNA gene MiSeq sequencing method. The soil bacterial α-diversity, which is represented by Chao1 index in terms of bacterial richness, was 783 ± 87 (mean ± SD) across all samples in this study. The N addition caused a decline in soil bacterial richness, most likely through its negative effect on soil pH. The decrease in soil pH resulted from the direct N input and indirect NO3− increase. However, the P treatment had no effect on soil bacterial richness. The NP treatment also reduced the soil bacterial richness as the N addition. These results suggested that the P input could not alleviate the loss of soil bacterial richness induced by excess N deposition in the old-growth N-rich tropical forest. The Acidobacteria, which comprised 31.1% of the soil bacterial community, were the most dominant bacteria across all samples. The addition of P shifted the soil bacterial community composition. The elevated P availability with P-addition and the decreased understory plant coverage in the N-input treatment altered the soil bacterial β-diversity. Our results highlight the different roles of N and P depositions in shaping the soil bacterial richness and community composition, thereby causing concomitant changes in understory plant and underground microbial communities in this ecosystem.
•A decrease in soil pH resulted from the direct N input and indirect NO3− increase.•N addition caused a decline in bacterial richness, possibly through its effect on pH.•Phosphorus addition shifted the soil bacterial community composition.•Elevated P availability and lower understory coverage altered bacterial community.•N and P additions play different roles in shaping bacterial richness and community.
Efforts to understand the environmental and biological factors that influence the dynamics of microbial communities have received substantial attention in microbial ecology. In this study, Illumina ...MiSeq high-throughput sequencing technology was used to examine the microbial community structure of activated sludge in municipal wastewater treatment systems (Chuzhou city, China). Overall, Proteobacteria, Chloroflexi, Actinobacteria, Acidobacteria, Actinobacteria, Bacteroidetes, and Firmicutes were the most dominant phyla in the five activated sludge samples. However, the community structure of nitrifying bacteria was relatively simple, and diversity was low; only AOB (Nitrosomonas) and NOB (Nitrospira) were detected. The dominant bacteria in the anaerobic sludge, anoxic sludge and oxic sludge were the same, and each bacterial species was relatively uniform, with differences only in proportions. Redundancy analysis indicated that pH, TP and COD were strong environmental factors influencing the bacterial community distribution. PICRUSt was used to describe the metabolic and functional abilities of the activated sludge bacterial communities. The results emphasized the vast genetic diversity of these organisms, which are involved in various essential processes such as amino acid transport and metabolism, energy production and conversion, cell wall/membrane/envelope/biogenesis, signal transduction mechanisms, and carbohydrate transport and metabolism. Activated sludge of municipal wastewater treatment systems can be ranked in the following order based on the 16S rRNA gene copy numbers of the detected phylotypes: S1 > S2 > S4 > S5 > S3. This study provides basic data and a theoretical analysis of the optimal design and operation in wastewater treatment plants.
Display omitted
•The first study on microbial community in Chuzhou Wastewater Treatment Plant.•Bacterial community structure of different treatment units was similar.•Only AOB (Nitrosomonas), NOB (Nitrospira) was detected.•Study on the microbial community structure can help engineers develop and optimize WWTP.
Nitrogen loss is the main problem in compost and controlling it is the key to the recovery and utilization of composted materials. This study systematically investigated the effect of nitrogen ...retaining microbial agent (NRMA) on nitrogen retention and the promotion of decay during manure composting and tested its effect on nitrogen conversion and bacterial community structure. During composting, various parameters were dynamically evaluated, including nitrogen loss and transformation, compost maturity and nutrient, microorganism population and bacteria community variation. Results showed that the inoculation of NRMA significantly reduced ammonia loss by 58.8% with 15 days shorter compost cycle. At the end of the composting, the total nitrogen (TN) and nitrate content of the experimental group were 23.3 g kg−1 and 4.5 g kg−1, 22.6% (p < 0.05) and 9.6% (p < 0.05) higher than those of the control group (19 g kg−1 and 4.1 g kg−1), respectively. In contrast, the ammonia emission and ammonium nitrogen in the experimental group (4.9 g and 1.4 g kg−1) were significant lower than those (11.9 g and 1.8 g kg−1) in the control group (p < 0.05). Nitrogen-transforming bacteria such as Paucisalibacillus, Sporosarcina, Sphingobacterium, and Oceanobacillus displayed obvious advantages at high temperatures, while Longispora and Luteivirga demonstrated clear benefits at the end of the compost. The mechanism of nitrogen loss reduction was proposed, which was regulated by the specific microorganisms in the compost, especially the strains from the NRMA. The strategy of addition NRMA shows great potential for industrial applications of manure compost, which could provide a novel alternative for the recovery of nitrogen resources from animal husbandry.
Display omitted
•Fertilization treatments affect soil aggregate fractionation.•Fertilization regimes influence phosphorus fraction.•Fertilization treatments affect P-cycling-related bacterial ...abundance.•Soil aggregate showed greater impact on P-cycling-related bacterial community than fertilization.•P components accounted for P-cycling-related bacterial community composition.
Fertilization could promote phosphorus (P) cycling in soil; however, it is unclear how long-term fertilization regimes affect P-cycling-related microbial communities in different soil aggregates. In this study, we compiled promising strategies to evaluate the effect of 40-year long-term fertilization treatments on the P-cycling-related bacterial communities associated with different soil aggregates, of which P fraction and physicochemical properties were also measured. We found that both organic and mineral fertilization treatments increased the proportion of silt + clay (< 53 μm) and decreased the proportion of macroaggregate (250–2000 μm). Organic fertilization increased microaggregate (53–250 μm) proportion while mineral fertilization resulted in the opposite. The abundances of phoC-, phoD-, phnX-, gcd-, and pstS-harboring bacteria increased in silt + clay in five fertilization treatments, while bpp-harboring bacterial abundance increased in microaggregate applied with nitrogen chemical fertilizer and nitrogen with combined manure fertilizer. Phytase activity was higher in macroaggregate in no fertilizer and mineral fertilization treatments, while phosphatase activity was higher in silt + clay in five fertilization treatments. Besides, fertilization significantly affected P fraction, with higher proportions of inorganic P, organic P, non-apatite inorganic P, and apatite inorganic P in silt + clay. For P-cycling-related bacterial community composition, 43.09% of the variation explained by fertilization treatment and aggregate fractionation, 73.92% of the variation explained by soil physicochemical properties and P fraction were found. Besides, P components especially organic P, non-apatite inorganic P, and labile P presented great effects on P-cycling-related bacterial community composition. To our knowledge, our findings first suggest that silt + clay is beneficial to enrich P-cycling-related bacteria, nutrient-driven aggregate fractionation and P fraction via fertilization treatments can shape P-cycling-related bacterial community composition.
Intercropping is an adapted farming system to optimize resource-use efficiency and crop yield, particularly in low input agricultural systems. Due to the beneficial eco-agricultural effects of grain ...legumes, their integration in mixed cropping systems such as intercropping systems can be more beneficial to soil fertility, soil functioning, and nutrient cycling. About 16–22% of the world’s food is provided by cropping systems. On smallholder farms in Eastern and Southern Africa, the integration of legumes has the potential to increase maize (Zea mays) production up to 35% (e.g., Maize-pigeon pea (Cajanus cajan) intercropping). Legume-based intercropping systems can also promote rhizobacterial community diversity and soil health by enhancing symbiotic and non-symbiotic beneficial population. In the rhizosphere, the bacterial community is required to improve the growth and health of both intercrops due to several “direct and indirect” mechanisms involving plant growth-promoting rhizobacteria (PGPR). This review aims to highlight the importance of both legume-based intercropping and root-associated microorganisms particular emphasis on rhizobacteria; since the whole “crop-crop-microorganism” system has the potential to improve crop agro-physiological performance. This study also discusses the key role of legumes as intercrops being fully synergistic with PGPR contributing to crop yield stability under stressful conditions, notably drought and nutrient deficiency. Thus, intercropping can be used as an agroecological practice to ensure the sustainability of production.
Display omitted
•The incorporation of legumes in cropping systems improves the physico-chemico-biological properties, soil fertility and ameliorate the resource use efficiency.•The intercropping based legumes enhance the chemotaxis and the behavior of beneficial root-associated bacteria in the rhizosphere.•The intercropping legume positively influences the interactive mechanisms between legumes and non-legumes and rhizobial strains in favor of both crops.•Adoption of legume-based intercropping systems and PGPR will sustainably improve crop agro-physiological performance.
Solar-driven advanced oxidation processes were studied in a pilot-scale photoreactor, as tertiary treatments of effluents from an urban wastewater treatment plant. Solar-H2O2, heterogeneous ...photocatalysis (with and/or without the addition of H2O2 and employing three different photocatalysts) and the photo-Fenton process were investigated. Chemical (sulfamethoxazole, carbamazepine, and diclofenac) and biological contaminants (faecal contamination indicators, their antibiotic resistant counterparts, 16S rRNA and antibiotic resistance genes), as well as the whole bacterial community, were characterized.
Heterogeneous photocatalysis using TiO2-P25 and assisted with H2O2 (P25/H2O2) was the most efficient process on the degradation of the chemical organic micropollutants, attaining levels below the limits of quantification in less than 4 h of treatment (corresponding to QUV < 40 kJ L−1). This performance was followed by the same process without H2O2, using TiO2-P25 or a composite material based on graphene oxide and TiO2.
Regarding the biological indicators, total faecal coliforms and enterococci and their antibiotic resistant (tetracycline and ciprofloxacin) counterparts were reduced to values close, or beneath, the detection limit (1 CFU 100 mL−1) for all treatments employing H2O2, even upon storage of the treated wastewater for 3-days. Moreover, P25/H2O2 and solar-H2O2 were the most efficient processes in the reduction of the abundance (gene copy number per volume of wastewater) of the analysed genes. However, this reduction was transient for 16S rRNA, intI1 and sul1 genes, since after 3-days storage of the treated wastewater their abundance increased to values close to pre-treatment levels. Similar behaviour was observed for the genes qnrS (using TiO2-P25), blaCTX-M and blaTEM (using TiO2-P25 and TiO2-P25/H2O2). Interestingly, higher proportions of sequence reads affiliated to the phylum Proteobacteria (Beta- and Gammaproteobacteria) were found after 3-days storage of treated wastewater than before its treatment. Members of the genera Pseudomonas, Rheinheimera and Methylotenera were among those with overgrowth.
Display omitted
•Different solar-driven advanced oxidation processes were studied at pilot-scale.•P25/H2O2 showed a best compromise to remove both chemical & biological pollutants.•P25/H2O2 didn't prevent reactivation of antibiotic resistant genes in stored water.•Beta- and Gammaproteobacteria relative abundance increased in stored treated water.
The profound intensification of agricultural practices by increased application of agro-chemicals, short crop rotations and ploughing resulted in loss of soil fertility, erosion and accumulation of ...soil-borne plant pathogens. Soil microbial communities are key players in ecosystem processes and are intimately linked to crop productivity and health. Thus a better understanding of how farming practices affect soil microbiota is needed in order to promote sustainable agriculture. The long-term field trial in Bernburg (Germany) established in 1992 provides a unique opportunity to assess the effects of i) the crop (maize vs. rapeseed) preceding the actual winter wheat culture, ii) tillage practice (mouldboard plough vs. cultivator tillage) and iii) standard nitrogen (N)-fertilization intensity with application of growth regulators and fungicides (intensive) compared to reduced N-fertilization without growth regulators and fungicides (extensive). We hypothesized that these different farming practices affect the soil prokaryotic community structures with consequences for their functional potential. Total community-DNA was extracted directly from soils sampled at wheat harvest. Illumina sequencing of 16S rRNA genes amplified from total community-DNA revealed a significant effect of tillage practice and the preceding crop on prokaryotic community structures, whereas the influence of N-fertilization intensity was marginal. A number of differentially abundant prokaryotic genera and their predicted functions between mouldboard plough vs. cultivator tillage as well as between different preceding crops were identified. Compared to extensive N-fertilization, intensive N-fertilization resulted in higher abundances of bacterial but not of archaeal amoA genes, that are involved in ammonia oxidation. Our data suggest that long-term farming strategies differently shape the soil prokaryotic community structure and functions, which should be considered when evaluating agricultural management strategies regarding their sustainability, soil health and crop performance.
•Long-term agricultural management leaves imprints on soil prokaryotic communities.•Effect of tillage and preceding crop stronger than fertilization intensity.•Predicted prokaryotic functional potentials differ among farming practices.
PDF
