Key Microbial Groups Research Articles

Dissolved greenhouse gases and benthic microbial communities in coastal wetlands of the Chilean coast semiarid region.

Coastal wetlands are ecosystems associated with intense carbon dioxide (CO2), methane (CH4) and nitrous oxide (N2O) recycling, modulated by salinity and other environmental factors that influence the microbial community involved in greenhouse gases production and consumption. In this study, we evaluated the influence of environmental factors on GHG concentration and benthic microbial community composition in coastal wetlands along the coast of the semiarid region. Wetlands were situated in landscapes along a south-north gradient of higher aridity and lower anthropogenic impact. Our results indicate that wetlands have a latitudinal variability associated with higher organic matter content at the north, especially in summer, and higher nutrient concentration at the south, predominantly in winter. During our sampling, wetlands were characterized by positive CO2 μM and CH4 nM excess, and a shift of N2O nM excess from negative to positive values from the north to the south. Benthic microbial communities were taxonomically diverse with > 60 phyla, especially in low frequency taxa. Highly abundant bacterial phyla were classified into Gammaproteobacteria (Betaproteobacteria order), Alphaproteobacteria and Deltaproteobacteria, including key functional groups such as nitrifying and methanotrophic bacteria. Generalized additive model (GAM) indicated that conductivity accounted for the larger variability of CH4 and CO2, but the predictions of CH4 and CO2 concentration were improved when latitude and pH concentration were included. Nitrate and latitude were the best predictors to account for the changes in the dissolved N2O distribution. Structural equation modeling (SEM), illustrated how the environment significantly influences functional microbial groups (nitrifiers and methane oxidizers) and their resulting effect on GHG distribution. Our results highlight the combined role of salinity and substrates of key functional microbial groups with metabolisms associated with both carbon and nitrogen, influencing dissolved GHG and their potential exchange in natural and anthropogenically impacted coastal wetlands.

Stressful, isolated, yet diverse: Green roofs have rich microbiomes that are not dominated by oligotrophic taxa.

Green roofs are unique ecosystems combining two major community assembly filters, namely stress and spatial isolation. As such, they represent an interesting model ecosystem in community ecology. In this study, we characterized the microbiome structure on 19 green roofs and 5 urban parks as a benchmark comparison (i.e. non-isolated, non-stressful habitats). Green roofs were not species depauperate, showing similar α-diversity compared to surrounding parks. We also did not find an overrepresentation of bacterial phyla typically recognized as oligotrophs, which calls into question the notion of green roofs as highly stressful habitats for bacteria, and/or the conservatism of nutritional ecophysiology at the phylum level. The geographical position of a roof, or its degree of spatial isolation (assessed through its height and area) were not important predictors of microbiome diversity and structure, suggesting that dispersal limitations impose little constraints on green roof microbiome assembly. Finally, key microbial groups (e.g. archaeal nitrifiers, Actinobacteria) were much less frequent and/or abundant on green roofs, which may have important implications for nutrient cycling and urban biogeochemistry. More work will be required to phenotype the microorganisms overrepresented on green roofs and specifically measure key soil processes in these unique urban ecosystems.

Characteristics and Assembly Process of Reclaimed Soil Microbial Communities in Eastern Plain Mining Areas

Understanding how soil microorganisms respond to land reclamation is essential to evaluating the success of ecological restoration actions in disturbed mine soil. However, the microbiological mechanism referred to as productivity reconstruction of the reclaimed soil is still unclear. To shed light on this mechanism, a total of 75 soil samples were collected for 16S rRNA amplicon high-throughput sequencing. The five sampling sites contained four reclamation plots (reclaimed 8 a, 11 a, 14 a, and 17 a) and 1 non-reclaimed plot, which served as the control sampling site. The microbial community composition, potential functions, and assembly mechanisms were also analyzed. The results showed that:①the richness of the microbial community increased with the reclamation time and was higher than that of the control site. However, the community diversity and evenness decreased with the increasing reclamation year (P<0.05). ②Acidobacteria, Chloroflexi, Proteobacteria, and Bacteroidetes dominated in the reclaimed soil, and the relative abundances of the first two phyla were significantly higher than that of the control (P<0.05), whereas the latter two presented the opposite trends (P<0.05). ③ Eight functions, including coenzyme transport and metabolism, translation, ribosomal structure, and biogenesis, showed a positive succession in the reclamation sites and enhanced with increasing reclamation years. ④ The molecular ecological networks of the microbial community in the plain mining area were well modular, whereas the key microbial groups belonged to the Acidobacteria and Bacteroidetes. The microbial communities were dominantly assembled with the deterministic process, and the homogeneous selection contributed the most, which might have been mainly controlled by the local special environment. The results presented herein will undoubtedly aid in the establishment of success indicators of ecological restoration activities in disturbed mining soil. These findings also provide the theoretical basis for improving the productivity and ecological services of reclaimed soil.

Microbial community composition, dynamics, and biogeochemistry during the start-up of a partial nitritation-anammox pathway in an upflow reactor

The dynamics of the microbial community and functional taxa related to nitrogen (N) removal biogeochemical processes can be important to the development of new cost-effective processes in wastewater treatment. This work consisted of the start-up of an upflow reactor for N-removal by partial nitritation/anammox pathway, working at ambient temperature, during 397 d. After an adaptation to the reactor operational conditions, a stable total N-removal (52% efficiency) was linked to ammonium deletion. High-throughput sequencing of 16S rRNA gene amplicons analysis revealed a relative abundance of about 1% of anammox genus Candidatus Brocadia after 397 d. Nitrosomonas, a nitrifying bacterium also increased the relative abundance, together with the accretion of relative numbers of Denitratisoma and Thiobacillus, recognized as heterotrophic and chemolithoautotrophic denitrifying bacteria, respectively. These findings provide a better understanding of the N-removal by key microbial groups that may be useful to optimize future field application of systems working at ambient temperature.

Effect of different microbial seeds on batch anaerobic digestion of fish waste

Initial microbial compositions would be the precursor for the efficient anaerobic digestion (AD) of fish waste (FW). A mesophilic batch test was conducted using four seeds collected from different digesters treating various combinations of substrates to investigate their effects on FW degradation. Key microbial groups were identified by 16s rRNA gene-based metagenomics analysis. Among four, the seed from the digester co-digesting livestock manure, food waste, and food wastewater showed the best performance and obtained the highest methane yield (350.5 ± 5.2 mL/gVSadded) and lowest lag phase (0.6 ± 0.1 d). Proteiniphilum, Aminobacterium, dgA-11 gut group, and Syntrophomonas were dominant bacterial genera identified in FW degradation. Methanosaeta was the dominant methanogen in the best performing seed and microbial network analysis revealed its contribution to achieving the highest CH4 yield. Obtained results could be useful in selecting microbial seed sources to avoid system imbalance in full-scale digesters that treat FW.

Mycorrhizal and rhizobial interactions influence model grassland plant community structure and productivity.

Arbuscular mycorrhizal (AM) fungi and rhizobium are likely important drivers of plant coexistence and grassland productivity due to complementary roles in supplying limiting nutrients. However, the interactive effects of mycorrhizal and rhizobial associations on plant community productivity and competitive dynamics remain unclear. To address this, we conducted a greenhouse experiment to determine the influences of these key microbial functional groups on communities comprising three plant species by comparing plant communities grown with or without each symbiont. We also utilized N-fertilization and clipping treatments to explore potential shifts in mycorrhizal and rhizobial benefits across abiotic and biotic conditions. Our research suggests AM fungi and rhizobium co-inoculation was strongly facilitative for plant community productivity and legume (Medicago sativa) growth and nodulation. Plant competitiveness shifted in the presence of AM fungi and rhizobium, favoring M. sativa over a neighboring C4 grass (Andropogon gerardii) and C3 forb (Ratibida pinnata). This may be due to rhizobial symbiosis as well as the relatively greater mycorrhizal growth response of M. sativa, compared to the other model plants. Clipping and N-fertilization altered relative costs and benefits of both symbioses, presumably by altering host-plant nitrogen and carbon dynamics, leading to a relative decrease in mycorrhizal responsiveness and proportional biomass of M. sativa relative to the total biomass of the entire plant community, with a concomitant relative increase in A. gerardii and R. pinnata proportional biomass. Our results demonstrate a strong influence of both microbial symbioses on host-plant competitiveness and community dynamics across clipping and N-fertilization treatments, suggesting the symbiotic rhizosphere community is critical for legume establishment in grasslands.

Methane-related community of a carbonate-enriched pockmark, Brazilian Southeastern continental slope

Pockmarks are geological features that often sustain hydrocarbon-related communities of microorganisms when active, seeping oil or methane. Microbial communities of inactive pockmarks have not been well studied until the present. Plenty of pockmarks in the Southwestern Atlantic Ocean have been discovered. However, no information is available about the organic characteristics in association with the microbial diversity related to methane and non-methane hydrocarbon consumption. This study examined the identity and potential ecology of the methane-related microbial community in an inactive SW Atlantic Carbonate-enriched Pockmark (SWACP). Undisturbed sediment cores were enriched with CH4 99.5% at 5°C, with samples harvested at 16h, 120h, 240h, 720h, and 960h, followed by metataxonomics functional prediction, and the correlation of microbial groups with incubation and enrichment types. The SWACP is depleted in organic compounds, and chemosynthetic production is dominant. Incubated mini-cores of sediment were affected by incubation time and enrichment type, which influenced the microbial composition. Although several taxa were shared among all sediment samples, specific groups per enrichment type and incubation time were observed. These communities comprised taxa previously reported in marine bottom waters, carbonate crusts, active cold-seeps, and inactive pockmarks. The methane-enriched taxa were predominantly related to aerobic methanotrophy, methylotrophy, aerobic and anaerobic non-methane hydrocarbon degradation, and fermentation. This study brings the first survey of the key microbial groups in methane fluxes of a Brazilian deep-sea pockmark, providing data for understanding the ecology surrounding the SW Atlantic gas field areas.

Enriched root bacterial microbiome in invaded vs native ranges of the model grass allotetraploid Brachypodium hybridum

Invasive species can shift the composition of key soil microbial groups, thus creating novel soil microbial communities. To better understand the biological drivers of invasion, we studied plant-microbial interactions in species of the Brachypodium distachyon complex, a model system for functional genomic studies of temperate grasses and bioenergy crops. While Brachypodium hybridum invasion in California is in an incipient stage, threatening natural and agricultural systems, its diploid progenitor species B. distachyon is not invasive in California. We investigated the root, soil, and rhizosphere bacterial composition of Brachypodium hybridum in both its native and invaded range, and of B. distachyon in the native range. We used high-throughput, amplicon sequencing to evaluate if the bacteria associated with these plants differ, and whether biotic controls may be driving B. hybridum invasion. Bacterial community composition of B. hybridum differed based on provenance (native or invaded range) for root, rhizosphere, and bulk soils, as did the abundance of dominant bacterial taxa. Bacteroidetes, Cyanobacteria and Bacillus spp. (species) were significantly more abundant in B. hybridum roots from the invaded range, whereas Proteobacteria, Firmicutes, Erwinia and Pseudomonas were more abundant in the native range roots. Brachypodium hybridum forms novel biotic interactions with a diverse suite of rhizosphere microbes from the invaded range, which may not exert a similar influence within its native range, ostensibly contributing to B. hybridum’s invasiveness. These associated plant microbiomes could inform future management approaches for B. hybridum in its invaded range and could be key to understanding, predicting, and preventing future plant invasions.

Diversity and potential function of bacterial communities during milk fermentation of Kazak artisanal cheese

Kazak artisanal cheese is a traditionally fermented food from the Uighur Autonomy Region of Xinjiang, China. In this study, we used Illumina MiSeq high-throughput sequencing technology to explore the microbial diversity during the milk fermentation of Kazak traditional hand-fermented cheese in Xinjiang, by analyzing the V3–V4 variable region of the bacterial 16S rRNA gene. Results showed that Lactobacillus and Lactococcus from the Firmicutes group comprised the dominant genera. Lactobacillus, Lactococcus, Acinetobacter, Anoxybacillus, Macrococcus, Acetobacter, Kurthia, Lelliottia, and Leuconostoc were identified as the key microbial groups during the milk fermentation of cheese. Correlation analysis also indicated that Lactobacillus had strong negative connections with Lactococcus, Acinetobacter, Macrococcus, Anoxybacillus, and Staphylococcus. The genera of Lactobacillus and Lactococcus (e.g., Lactobacillus paracasei B1, Lactobacillus sp. B4 and Lactococcus lactis B11) had higher enzyme activity characteristics according to the enzyme activity experiments. Subsequent gene function prediction indicated that the microorganisms in fermented milk products mainly contributed to carbohydrate and amino acid metabolism, which might be closely related to the development of the flavor of the cheese. Our study provides a theoretical basis for understanding the succession of bacteria and the application of potential functional microorganisms in Kazak cheese.

Bacterial Community Structure and Dynamic Changes in Different Functional Areas of a Piggery Wastewater Treatment System.

Chemicals of emerging concern (CEC) in pig farm breeding wastewater, such as antibiotics, will soon pose a serious threat to public health. It is therefore essential to consider improving the treatment efficiency of piggery wastewater in terms of microorganisms. In order to optimize the overall piggery wastewater treatment system from the perspective of the bacterial community structure and its response to environmental factors, five samples were randomly taken from each area of a piggery’s wastewater treatment system using a random sampling method. The bacterial communities’ composition and their correlation with wastewater quality were then analyzed using Illumina MiSeq high-throughput sequencing. The results showed that the bacterial community composition of each treatment unit was similar. However, differences in abundance were significant, and the bacterial community structure gradually changed with the process. Proteobacteria showed more adaptability to an anaerobic environment than Firmicutes, and the abundance of Tissierella in anaerobic zones was low. The abundance of Clostridial (39.02%) and Bacteroides (20.6%) in the inlet was significantly higher than it was in the aerobic zone and the anoxic zone (p < 0.05). Rhodocyclaceae is a key functional microbial group in a wastewater treatment system, and it is a dominant microbial group in activated sludge. Redundancy analysis (RDA) showed that chemical oxygen demand (COD) had the greatest impact on bacterial community structure. Total phosphorus (TP), total nitrogen (TN), PH and COD contents were significantly negatively correlated with Sphingobacteriia, Betaproteobacteria and Gammaproteobacteria, and significantly positively correlated with Bacteroidia and Clostridia. These results offer basic data and theoretical support for optimizing livestock wastewater treatment systems using bacterial community structures.

Steering microbiomes by organic amendments towards climate-smart agricultural soils

We steered the soil microbiome via applications of organic residues (mix of cover crop residues, sewage sludge + compost, and digestate + compost) to enhance multiple ecosystem services in line with climate-smart agriculture. Our result highlights the potential to reduce greenhouse gases (GHG) emissions from agricultural soils by the application of specific organic amendments (especially digestate + compost). Unexpectedly, also the addition of mineral fertilizer in our mesocosms led to similar combined GHG emissions than one of the specific organic amendments. However, the application of organic amendments has the potential to increase soil C, which is not the case when using mineral fertilizer. While GHG emissions from cover crop residues were significantly higher compared to mineral fertilizer and the other organic amendments, crop growth was promoted. Furthermore, all organic amendments induced a shift in the diversity and abundances of key microbial groups. We show that organic amendments have the potential to not only lower GHG emissions by modifying the microbial community abundance and composition, but also favour crop growth-promoting microorganisms. This modulation of the microbial community by organic amendments bears the potential to turn soils into more climate-smart soils in comparison to the more conventional use of mineral fertilizers.

Partitioning of nutrient removal contribution between granules and flocs in a hybrid granular activated sludge system

Sludge granulation in continuous-flow systems is an emerging technology to intensify existing activated sludge infrastructure for nutrient removal. In these systems, the nutrient removal contributions and partitioning of microbial functions between granules and flocs can offer insights into process implementations. To this end, a reactor system that simulates the continuous-flow environment using an equal amount of initial granule and floc biomass was investigated. The two operational strategies for maintaining granule growth in the continuous-flow system were (a) the higher solids retention time (SRT) for the granules versus flocs, as well as (b) selective feeding of carbon to the granules. The SRT of the large granule fractions (>425 µm, LG) and floc/small granule fractions (<425 µm, FSG) were controlled at 20 and 2.7–6.0 days, respectively. Long term operation of the hybrid granule/floc system achieved high PO43- and NH4+ removal efficiencies. Higher polyphosphate-accumulating organisms (PAO) activity was observed in the FSG than LG, while ammonia-oxidizing bacteria (AOB) activities were similar in the two biomass fractions. Nitrite shunt was observed in the FSG, possibly due to out-competition by the high NOB activity in LG. More importantly, washing out the FSG caused a reduction in LG's AOB and PAO activity, indicating a possible dependency of LG on FSG for maintaining its nutrient removal capacity. Our findings highlighted the partitioning and potential competition/cooperation of key microbial functional groups between LG and FSG, facilitating nutrient removal in a hybrid granular activated sludge system, as well as implications for practical application of the treatment platform.

Ditching Nutrients: Roadside Drainage Networks are Hotspots for Microbial Nitrogen Removal

AbstractHuman‐made stormwater control systems are biogeochemical hotspots, but construction and management may result in homogenization of their ecosystem structure. Roadside ditches are a ubiquitous part of the landscape, yet few studies have quantified their biogeochemical potential. We conducted a study to determine (a) nitrate (NO3−) removal potential through rate measurements and (b) microbial community structure using 16S rRNA gene (iTag) sequencing in roadside ditches draining predominantly forested, urban, and agricultural watersheds surrounding Mobile Bay, AL (USA). We found that nitrogen (N) removal rates by denitrification and anammox dominated over N‐retention by dissimilatory nitrate reduction to ammonium, accounting for upwards of 89% of NO3− reduction on average. There were no differences in soil characteristics between land use types, but denitrification potential rates in forested ditches were less than half of those in urban and agricultural ditches, possibly as a result of differences in vegetation management. Microbial alpha and beta diversity were largely homogenous across the three land use types. However, indicator species analysis revealed putative ammonia oxidizers (Nitrososphaeraceae and Nitrosomonadaceae), nitrate reducers (Gaiellales), and nitrous oxide reducers (Myxococcales) as significant groups in urban and agricultural ditches. We conclude that land use effects on N‐removal in these constructed drainage networks are mediated through key microbial groups and ditch vegetation management strategies. Further, roadside ditches have significant potential for reactive N removal in the landscape.

Destruction of the soil microbial ecological environment caused by the over-utilization of the rice-crayfish co-cropping pattern

The rice-crayfish co-cropping pattern is a traditional method for the intensive utilization of rice fields. In recent years, this pattern has been over-developed in many countries and regions, especially in China, because of its simple agronomic technology and high economic benefits. However, little is known about the potential ecological problems regarding soil microorganisms caused by the over-utilization of this pattern. The results show that rice-crayfish co-cropping, when over-utilized for a long time, reduced soil microbial richness and diversity compared with rice monocropping. A decrease in bacterial abundance in the nitrogen cycle and an increase in bacterial abundance in the carbon cycle led to a decrease in the nitrogen cycle function and an increase in the carbon cycle function. In an analysis of bacteria that are sensitive to cropping patterns, it was found that in the rice-crayfish co-cropping, the relative abundances of sensitive OTUs from Firmicutes (Bacillus and Clostridium) and Chloroflexi (Anaerolineaceae) were significantly higher during the entire growth period than those observed in the rice monocropping pattern, while the relative abundances of sensitive OTUs from Nitrospirae (Nitrospira), Gemmatimonadetes (Gemmatimonas), and Actinobacteria (Nocardioides) were significantly lower than those observed in the rice monocropping pattern. A network analysis shows that growth-period-sensitive OTUs drive the co-occurrence network modules, although the OTUs also have positive and negative correlations among modules but a positive synergistic effect on the regulation of soil nutrients. In addition, OTUs that were sensitive at the booting stage and filling stage were the key microbial groups in the rice-crayfish co-cropping and rice monocropping networks, respectively. Understanding the classifications and functions of sensitive microbes present during the rice growth period is the basis for formulating a microbial flora management strategy for the rice-crayfish co-cropping pattern, which is of great significance for adjusting agricultural management measures and controlling current soil microbial ecological problems.

Linking seasonal N2O emissions and nitrification failures to microbial dynamics in a SBR wastewater treatment plant

Nitrous oxide (N2O) is a strong greenhouse gas and causal for stratospheric ozone depletion. During biological nitrogen removal in wastewater treatment plants (WWTP), high N2O fluxes to the atmosphere can occur, typically exhibiting a seasonal emission pattern. Attempts to explain the peak emission phases in winter and spring using physico-chemical process data from WWTP were so far unsuccessful and new approaches are required. The complex and diverse microbial community of activated sludge used in biological treatment systems also exhibit substantial seasonal patterns. However, a potentially causal link between the seasonal patterns of microbial diversity and N2O emissions has not yet been investigated. Here we show that in a full-scale WWTP nitrification failure and N2O peak emissions, bad settleability of the activated sludge and a turbid effluent strongly correlate with a significant reduction in the microbial community diversity and shifts in community composition. During episodes of impaired performance, we observed a significant reduction in abundance for filamentous and nitrite oxidizing bacteria in all affected reactors. In some reactors that did not exhibit nitrification and settling failures, we observed a stable microbial community and no drastic loss of species. Standard engineering approaches to stabilize nitrification, such as increasing the aerobic sludge age and oxygen availability failed to improve the plant performance on this particular WWTP and replacing the activated sludge was the only measure applied by the operators to recover treatment performance in affected reactors. Our results demonstrate that disturbances of the sludge microbiome affect key structural and functional microbial groups, which lead to seasonal N2O emission patterns. To reduce N2O emissions from WWTP, it is therefore crucial to understand the drivers that lead to the microbial population dynamics in the activated sludge.

Sulfate addition and rising temperature promote arsenic methylation and the formation of methylated thioarsenates in paddy soils

Microbe-mediated arsenic (As) methylation is enhanced when paddy soils are flooded, producing primarily dimethylarsinic acid (DMA) that is phytotoxic and can induce rice straighthead disease. Thiolation of DMA produces methylated thioarsenate compounds such as di-methylated monothioarsenate (DMMTA) and di-methylated dithioarsenate (DMDTA), the former is highly toxic to humans. In the present study, we investigated the factors that influenced As methylation and thiolation in two paddy soils in which rice crops showed straighthead disease symptoms and contained high levels of DMA in the grains. Under flooded incubation conditions, the concentrations of various methylated and thio-methylated As species in the soil porewater increased rapidly when the redox potential decreased from approximately 0 to −100 mV, and their concentrations declined thereafter. Sulfate addition increased the copy numbers of dissimilatory sulfite reductase β-subunit (dsrB) genes and arsenite S-adenosylmethionine methyltransferase genes (arsM), and the production of DMA, DMMTA and DMDTA. Rising temperature also increased dsrB and arsM copy numbers, increased and advanced the peak concentrations of DMA, DMMTA and DMDTA production. Sulfate addition produced larger effects on dsrB and arsM copy numbers and As methylation at the higher temperature. There were significant correlations between dsrB and arsMcopy numbers, and between DMA and DMMTA or DMDTA concentrations, with DMMTA and DMDTA on average representing 36% and 6% of DMA, respectively. These results suggest that sulfate reducing bacteria are the key microbial group driving both the As methylation and thiolation processes in flooded paddy soils.

植物-土壤反馈与草地群落演替:菌根真菌和土壤病原菌的调控作用

由植物引起的根际土壤生物或非生物环境的改变能够反馈影响群落中不同植物的生长，直接改变共存植物的相对竞争关系，推动群落结构的动态变化。作为土壤生物群落的重要组成部分，土壤微生物在植物-土壤反馈关系中起到重要的调控作用，对解释植物群落的演替进程和方向有着重要的意义。在草地植物群落演替的早期阶段和外来物种入侵的过程中，宿主植物对丛枝菌根真菌（AMF）的依赖性较低，受本地病原菌的影响较小，一般不存在负反馈。在演替后期，植物对AMF更具依赖性，而积累的病原菌则产生较强的负反馈效应，从而促进群落物种共存和植物多样性，提高草地生产力和稳定性。研究微生物-植物反馈机制不仅有助于完善草地退化与恢复理论，还对退化草地恢复治理的实践有着指导意义。未来关于根际微生物-植物反馈在草地群落演替中的作用应该加强以下几方面的研究：（1）在实验方法上，开展专性微生物-植物反馈研究；（2）在测定指标上，进一步量化不同微生物在反馈关系中的功能差异；（3）在研究对象上，加强土壤微生物在植物群落水平的反馈研究；（4）在应用上，明晰植物-土壤反馈在退化草地恢复过程中的作用，指导草地管理实践。;Biotic and abiotic changes of soil properties (e.g. physical, chemical and biotic) caused by a plant affect the growth of other plant species within the same communities, reshape the competitive relationship between different species, and restructure the dynamic changes of species composition. The feedback between plant and soil has become an important concept for explaining the diversity, stability, dynamics and succession of plant communities. Its process and mechanism are also key scientific issues to understand the responses of terrestrial ecosystems to global changes. However, biotic factors, in particular soil microbes mediated plant-soil feedback are still poorly understood. These changes in key microbial groups, such as arbuscular mycorrhizal fungi (AMF) and soil pathogens may increase or decrease the plant growth, resulting in positive or negative plant-soil feedbacks. In the early successional stage or during exotic plant invasion, host plants preferentially utilizing abundant soil nutrients have low dependence on the AMF and are less affected by native pathogens. Generally, there is no negative feedback. In the late successional stage, as the nutrients are being depleted, AMF help host plants with better access to soil nutrients and increased resistance to stress and pathogens, which could generate positive feedback and potentially accelerate succession. However, the accumulated pathogens can generate negative feedback and contribute to plant species coexistence and diversity, and thus improved productivity and stability of grassland. The study of microbial feedbacks on plant community dynamic is not only helpful to improve the theory of grassland degradation and restoration, but also instructive to the practice of restoration and management of degraded grassland. In the future, the key issues of plant-microbe feedback in grassland community succession were suggested as follows. (1)In experimental methods, it is necessary to test the net effect of obligate microbes dynamics on the plant succession using a fully reciprocal inoculation experiment which involves host-mediated differentiation of microbial communities and differential effects of the microbes on the plant fitness. (2)Regarding measurement indexes, further work quantizing the trade-off between the nutrient uptake and the carbon allocated to the microbes by host plant is needed. Comparing the ratios of nutrient benefit versus carbon cost between plants reciprocally inoculated with own and foreign microbial communities would enable us to evaluate functional variation between different microbes. (3)For research objects, the impacts of microbes on plant community structure require more empirical attention. In terms of application, the role of plant-microbe feedback on the restoration of degraded grassland is clarified to guide grassland management.

FISH investigation of the bacterial groups anammox and Azoarcus-Thauera at treatment of landfill leachate

The landfill leachate is heavily polluted wastewater produced in the landfills. The management of the purification of the leachate is especially challenging and that is why new approaches and indicators are needed. The quantity, localization, interaction, clustering of the key microbial groups, responsible for the critical transformation processes can be used as indication leading to better performance of the technology. This study is focused on two bacterial groups (Anammox and Azoarcus-Thauera cluster) which have potential to serve as indicators for the landfill leachate treatment. Their quantity and activity were studied by FISH during lab-scale treatment of leachate from the Municipal Enterprise for Waste Treatment (MEWT), Sofia, Bulgaria. Two activated sludges (AS) were used – one from the MEWT and another form the WWTP (wastewater treatment plant) of Sofia. The obtained results showed that 74% of the COD was eliminated when leachate was diluted 50 and 25 times and 31% - when undiluted leachate was used. At the end of the process (21 day) the Azoarcus-Thauera group formed large aggregations in the AS from MEWT. They were 17.50% of the bacteria there while in the AS from the WWTP of Sofia they represented only 2.61%. The quantity of the anammox bacteria remained almost unchanged during the process and was 10.75% of the community from MEWT which eliminated 98 mg/L more ammonium ions at the end of the process and 6% from the community from the WWTP of Sofia. The two studied groups gave more complex information about the processes in the AS related to the elimination of the nitrogen and carbon containing pollutants. They could be used for better management of the biological processes during landfill leachate treatment. Key words: landfill leachate; anammox, Azoarcus-Thauera; activated sludge; fluorescence in-situ hybridization

Larger Anammox Granules not only Harbor Higher Species Diversity but also Support More Functional Diversity.

Granule-based partial nitritation and anammox (PN/A) represents one of the most energy-efficient biotechniques for ammonium removal from wastewater. The PN/A granules appear in a continuum of sizes, yet little is known about the extent to which microbial communities and microbial metabolisms are partitioned between size-fractionated granules. Here, we divided granules harvested from a pilot-scale PN/A reactor into five discrete size fractions (<0.2, 0.2-0.5, 0.5-0.8, 0.8-1.0, and >1.0 mm). The composition and functional attribute of five pools of the size-fractionated granules were characterized by 16S ribosomal RNA (rRNA) gene amplicon and metagenomic and metatranscriptomic sequencing to provide a comprehensive insight into the key microbial group in a PN/A system. Larger granules were shown to not only harbor higher microbial diversity but also support more diverse functions than smaller granules. De novo coassembly and binning of metagenomic reads yielded 22 draft genomes of dominant microorganisms, which allowed us to infer an ecological model of the microbial ecosystem in anammox-based granules. This genome-based ecological model indicates that nitrifying organisms in smaller granules feed nitrite to anammox bacteria in larger granules. The results improve our understanding of the PN/A system, especially for the metabolic interactions between small and large granules.

Rhizospheric microbiomes help Dongxiang common wild rice (Oryza rufipogon Griff.) rather than Leersia hexandra Swartz survive under cold stress

ABSTRACT Dongxiang common wild rice (CWR) is extremely cold tolerant, which can grow at the northernmost latitudes. To take full advantage of Dongxiang CWR’s cold tolerance for rice production and breeding, it is important to obtain a deep understanding of the mechanism underlying its cold tolerance. In this study, the rhizospheric microbiome of CWR was investigated and compared with that of Leersia hexandra Swartz (LHS) in Dongxiang to clarify the role of the rhizospheric microbiome in CWR cold tolerance. The results showed that, compared with the LHS rhizospheric microbiome, the CWR rhizospheric microbiome was less diverse and smaller, as indicated by its lower diversity and richness indices and fewer detected groups, core genera, and indicator genera. However, a larger proportion of the CWR indicator genera and unique genera, including Acidiphilium, Mortierella, Glomus, etc. showed the ability to adapt to low temperatures, indicating that CWR was more likely to be associated with microbial groups that may enhance cold tolerance. The results indicated that the extreme cold tolerance of Dongxiang CWR benefited from its rhizospheric microbiome, and this cold tolerance was speculated to benefit more from key microbial groups (indicator genera and unique genera) than from microbial diversity.