Syntrophic-archaeal associations in a nutrient-impacted freshwater marsh

Partial nitrification and simultaneous denitrification in sequential anaerobic and aerobic reactors: performance and microbial community dynamics

ABSTRACTThe removal of organic matter and nitrogen from domestic sewage was evaluated using a system composed of two sequential reactors: an anaerobic reactor (ANR) with suspended sludge and an aerobic (AER) reactor with suspended and adhered sludge to polyurethane foams. Nitrogen removal consisted of AER operating at low dissolved oxygen (DO) concentrations; this favoured the simultaneous nitrification and denitrification (SND) process. The concentration of COD and N were 440 mgO2.L-1 and 37 mgTN.L-1, respectively. The operation was divided into three phases (P), lasting 51, 53, and 46 days, respectively. The initial DO concentrations applied in the AER were: 3.0 (PI) and 1.5 mg.L-1 (PII and PIII). In PIII, the AER effluent was recirculated to the ANR at a ratio of 0.25. Kinetic assays were performed to determine the nitrification and denitrification rates of the biomasses (ANR and AER in PIII). Changes in the microbial community were evaluated throughout phases PI to PIII by massive sequencing. In PIII, the best results obtained for chemical oxygen demand (COD) and total nitrogen (TN-N) removal efficiencies, were close to 94% and 65%, respectively. Under these conditions, system effluent concentrations below 30 mg COD.L-1 and 15 mg TN-N.L-1 were verified. The nitritation and nitration rates were 10.5 and 6.5 mg N.g VSS-1.h-1, while the denitrification via nitrite and nitrate were 6.8 and 5.8 mg N.g VSS-1.h-1, respectively. A mixotrophic community was prevalent, with Rhodococcus, Nitrosomonas, Pseudomnas, and Porphyromonas being dominant or co-dominant in most of the samples, confirming the SND process in the AER sludge.

Cooperative microbial interactions mediate community biogeochemical responses to saltwater intrusion in wetland soils

In freshwater wetlands, competitive and cooperative interactions between respiratory, fermentative, and methanogenic microbes mediate the decomposition of organic matter. These interactions may be disrupted by saltwater intrusion disturbances that enhance the activity of sulfate-reducing bacteria (SRB), intensifying their competition with syntrophic bacteria and methanogens for electron donors. We simulated saltwater intrusion into wetland soil microcosms and examined biogeochemical and microbial responses, employing metabolic inhibitors to isolate the activity of various microbial functional groups. Sulfate additions increased total carbon dioxide production but decreased methane production. Butyrate degradation assays showed continued (but lower) levels of syntrophic metabolism despite strong demand by SRB for this key intermediate decomposition product and a shift in the methanogen community toward acetoclastic members. One month after removing SRB competition, total methane production recovered by only ∼50%. Similarly, butyrate assays showed an altered accumulation of products (including less methane), although overall rates of syntrophic butyrate breakdown largely recovered. These effects illustrate that changes in carbon mineralization following saltwater intrusion are driven by more than the oft-cited competition between SRB and methanogens for shared electron donors. Thus, the impacts of disturbances on wetland biogeochemistry are likely to persist until cooperative and competitive microbial metabolic interactions can recover fully.

Characterization of Bacterial and Fungal Communities Reveals Novel Consortia in Tropical Oligotrophic Peatlands

Despite their importance for global biogeochemical cycles and carbon sequestration, the microbiome of tropical peatlands remains under-determined. Microbial interactions within peatlands can regulate greenhouse gas production, organic matter turnover, and nutrient cycling. Here we analyze bacterial and fungal communities along a steep P gradient in a tropical peat dome and investigate community level traits and network analyses to better understand the composition and potential interactions of microorganisms in these understudied systems and their relationship to peatland biogeochemistry. We found that both bacterial and fungal community compositions were significantly different along the P gradient, and that the low-P bog plain was characterized by distinct fungal and bacterial families. At low P, the dominant fungal families were cosmopolitan parasites and endophytes, including Clavicipitaceae (19%) in shallow soils (0-4 cm), Hypocreaceae (50%) in intermediate-depth soils (4-8 cm), and Chaetothyriaceae (45%) in deep soils (24-30 cm). In contrast, high- and intermediate-P sites were dominated by saprotrophic families at all depths. Bacterial communities were consistently dominated by the acidophilic Koribacteraceae family, with the exception of the low-P bog site, which was dominated by Acetobacteraceae (19%) and Syntrophaceae (11%). These two families, as well as Rhodospirillaceae, Syntrophobacteraceae, Syntrophorhabdaceae, Spirochaetaceae, and Methylococcaceae appeared within low-P bacterial networks, suggesting the presence of a syntrophic-methanogenic consortium in these soils. Further investigation into the active microbial communities at these sites, when paired with CH₄ and CO₂ gas exchange, and the quantification of metabolic intermediates will validate these potential interactions and provide insight into microbially driven biogeochemical cycling within these globally important tropical peatlands.

Microbial Community Structure and Associations During a Marine Dinoflagellate Bloom

Interactions between microorganisms and algae during bloom events significantly impacts their physiology, alters ambient chemistry, and shapes ecosystem diversity. The potential role these interactions have in bloom development and decline are also of particular interest given the ecosystem impacts of algal blooms. We hypothesized that microbial community structure and succession is linked to specific bloom stages, and reflects complex interactions among taxa comprising the phycosphere environment. This investigation used pyrosequencing and correlation approaches to assess patterns and associations among bacteria, archaea, and microeukaryotes during a spring bloom of the dinoflagellate Alexandrium catenella. Within the bacterial community, Gammaproteobacteria and Bacteroidetes were predominant during the initial bloom stage, while Alphaproteobacteria, Cyanobacteria, and Actinobacteria were the most abundant taxa present during bloom onset and termination. In the archaea biosphere, methanogenic members were present during the early bloom period while the majority of species identified in the late bloom stage were ammonia-oxidizing archaea and Halobacteriales. Dinoflagellates were the major eukaryotic group present during most stages of the bloom, whereas a mixed assemblage comprising diatoms, green-algae, rotifera, and other microzooplankton were present during bloom termination. Temperature and salinity were key environmental factors associated with changes in bacterial and archaeal community structure, respectively, whereas inorganic nitrogen and inorganic phosphate were associated with eukaryotic variation. The relative contribution of environmental parameters measured during the bloom to variability among samples was 35.3%. Interaction analysis showed that Maxillopoda, Spirotrichea, Dinoflagellata, and Halobacteria were keystone taxa within the positive-correlation network, while Halobacteria, Dictyochophyceae, Mamiellophyceae, and Gammaproteobacteria were the main contributors to the negative-correlation network. The positive and negative relationships were the primary drivers of mutualist and competitive interactions that impacted algal bloom fate, respectively. Functional predictions showed that blooms enhance microbial carbohydrate and energy metabolism, and alter the sulfur cycle. Our results suggest that microbial community structure is strongly linked to bloom progression, although specific drivers of community interactions and responses are not well understood. The importance of considering biotic interactions (e.g., competition, symbiosis, and predation) when investigating the link between microbial ecological behavior and an algal bloom's trajectory is also highlighted.

Spatiotemporal variation of bacterial and archaeal communities in sediments of a drinking reservoir, Beijing, China

Bacterial and archaeal assemblages are one of the most important contributors to the recycling of nutrients and the decomposition of organic matter in aquatic sediments. However, their spatiotemporal variation and its driving factors remain unclear, especially for drinking reservoirs, which are strongly affected by human consumption. Using quantitative PCR and Illumina MiSeq sequencing, we investigated the bacterial and archaeal communities in the sediments of a drinking reservoir, the Miyun Reservoir, one of the most important drinking sources for Beijing City. The abundance of bacteria and archaea presented no spatiotemporal variation. With respect to community diversity, visible spatial and temporal differences were observed in archaea, whereas the bacterial community showed minor variation. The bacterial communities in the reservoir sediment mainly included Proteobacteria, Bacteroidetes, Nitrospirae, Acidobacteria, and Verrucomicrobia. The bacterial community structure showed obvious spatial variation. The composition of the bacterial operational taxonomic units (OTUs) and main phyla were dam-specific; the composition of samples in front of the dam were significantly different from the composition of the other samples. The archaeal communities were mainly represented by Woesearchaeota and Euryarchaeota. Distinctly spatial and seasonal variation was observed in the archaeal community structure. The sediment NH₄⁺-N, pH, and water depth were identified as the key driving factors of changes in the composition of the bacterial and archaeal communities. Water depth might have the greatest influence on the microbial community structure. The dam-specific community structure may be related to the greater water depth in front of the dam. This finding indicates that water depth might be the greatest contributor to the microbial community structure in the Miyun Reservoir.

EFFECT OF COD LOADING RATE ON AN UPFLOW ANAEROBIC SLUDGE BLANKET REACTOR DURING ANAEROBIC DIGESTION OF PALM OIL MILL EFFLUENT WITH BUTYRATE / SUVARTOJAMO CHDS POVEIKIS PALMIŲ ALIEJAUS GAMYBINIŲ NUOTEKŲ SU BUTIRATU ANAEROBINIO PŪDYMO PLOKŠTELINIAME REAKTORIUJE METU

Palm oil Mill Effluent (POME) with concentrated butyrate was treated in a 4.5 l upflow anaerobic sludge blanket reactor (UASBR), run over a range of influent concentrations (16.5–46.0 g-COD l−1), chemical oxygen demand (COD) loading rates (1.5–11.5 g-CODl−1d−1) and 11–4 days hydraulic retention time (HRT) at 37 °C by maintaining pH between 6.5–7.5. The process consistently removed 97–99% of COD at loading rates up to 1.5–4.8 g-COD l−1d−1 by varying HRT (11–7.2 days). Butyrate is an important intermediate in the anaerobic degradation of organic matter. In sulphate-depleted environment, butyrate in POME (BOD/COD ratio of 0.5) is β-oxidised to acetate and hydrogen, by obligate proton reducers in syntrophic association with hydrogen utilizing methanogens. The conversion of acetate to methane appeared to be rate limiting step. Maximum biogas (20.17 ll−1d−1) and methane production (16.2 ll−1d−1) were obtained at COD loading rate of 4.80 gl−1d−1and HRT of 7.2 days. The biogas and methane production were higher in the presence of butyrate compared to control. The methane content of the biogas was in the range of 70–80% throughout the study while in control it was 60–65%. Finding of this study clearly indicates the successful treatment of POME with butyrate in UASBR. Santrauka Palmių aliejaus gamybinės nuotekos (POME) su koncentruotu butiratu buvo apdorotos 4,5 l talpos aukštyn tekančio aerobinio dumblo plokšteliniame reaktoriuje (UASBR). Nuotekos tekėjo įvairių koncentracijų (16,5–46,0 g – ChDS 1−1), cheminio deguonies suvartojimo (ChDS) normos (1,5–11,5 g – ChDS 1−1d.−1). Hidraulinio sulaikymo trukmė (HRT) nuo 11 iki 4 dienų, kai temperatūra 37 °C, pH palaikant 6,5–7,5. Vykstant procesui nuolat buvo pašalinama 97–99% ChD, kai tiekimo ir pakrovimo sparta 1,5–4,8 g – ChDS 1−1d.−1 kintant HRT(11–7,2 d.). Butiratas yra svarbus tarpininkas organinių medžiagų anaerobinio skilimo procese. Sulfatas iš aplinkos, butiratas iš POME (BDS/ChDS santykis 0,5) yra acetato ir vandenilio β oksidatoriai, priverčiantys protonų reducentus sintrofinės sąveikos su vandeniliu metu utilizuoti metanogenus. Acetato virtimas metanu pasirodė esąs greitį ribojantis veiksnys. Daugiausia biodujų (20,17 l 1−1 d.−1) ir metano (16,2 l 1−1 d.−1) susidarė tada, kai suvartojamo ChD tiekimo greitis buvo 4,80 g 1−1d.−1, o HRT – 7,2 dienos. Daugiau biodujų ir metano susidarė dalyvaujant butiratui, palyginti su kontroliniu pavyzdžiu. Biodujose metano kiekis tyrimo metu svyravo 70–80%, o kontroliniame buvo 60–65%. Šis tyrimas aiškiai parodė, kad POME su butiratu UASBreaktoriuje apdorojamas sėkmingai.

Microbial and geochemical assessment of bauxitic un-mined and post-mined chronosequence soils from Mocho Mountains, Jamaica

Microorganisms are very sensitive to environmental change and can be used to gauge anthropogenic impacts and even predict restoration success of degraded environments. Here, we report assessment of bauxite mining activities on soil biogeochemistry and microbial community structure using un-mined and three post-mined sites in Jamaica. The post-mined soils represent a chronosequence, undergoing restoration since 1987, 1997, and 2007. Soils were collected during dry and wet seasons and analyzed for pH, organic matter (OM), total carbon (TC), nitrogen (TN), and phosphorus. The microbial community structure was assessed through quantitative PCR and massively parallel bacterial ribosomal RNA (rRNA) gene sequencing. Edaphic factors and microbial community composition were analyzed using multivariate statistical approaches and revealed a significant, negative impact of mining on soil that persisted even after greater than 20 years of restoration. Seasonal fluctuations contributed to variation in measured soil properties and community composition, but they were minor in comparison to long-term effects of mining. In both seasons, post-mined soils were higher in pH but OM, TC, and TN decreased. Bacterial rRNA gene analyses demonstrated a general decrease in diversity in post-mined soils and up to a 3-log decrease in rRNA gene abundance. Community composition analyses demonstrated that bacteria from the Proteobacteria (α, β, γ, δ), Acidobacteria, and Firmicutes were abundant in all soils. The abundance of Firmicutes was elevated in newer post-mined soils relative to the un-mined soil, and this contrasted a decrease, relative to un-mined soils, in proteobacterial and acidobacterial rRNA gene abundances. Our study indicates long-lasting impacts of mining activities to soil biogeochemical and microbial properties with impending loss in soil productivity.

Soil functional diversity analysis of a bauxite-mined restoration chronosequence

Soil microorganisms are sensitive to environmental perturbations such that changes in microbial community structure and function can provide early signs of anthropogenic disturbances and even predict restoration success. We evaluated the bacterial functional diversity of un-mined and three chronosequence sites at various stages of rehabilitation (0, 10, and 20 years old) located in the Mocho Mountains of Jamaica. Samples were collected during the dry and wet seasons and analyzed for metal concentrations, microbial biomass carbon, bacterial numbers, and functional responses of soil microbiota using community-level physiological profile (CLPP) assays. Regardless of the season, un-mined soils consisted of higher microbial biomass and numbers than any of the rehabilitated sites. Additionally, the number and rate of substrates utilized and substrate evenness (the distribution of color development between the substrates) were significantly greater in the un-mined soils with carbohydrates being preferentially utilized than amino acids, polymers, carboxylic acids, and esters. To some extent, functional responses varied with the seasons but the least physiological activity was shown by the site rehabilitated in 1987 indicating long-term perturbation to this ecosystem. Small subunit ribosomal DNA (SSUrDNA)-denaturing gradient-gel electrophoresis analyses on the microbiota collected from the most preferred CLPP substrates followed by taxonomic analyses showed Proteobacteria, specifically the gamma-proteobacteria, as the most functionally active phyla, indicating a propensity of this phyla to out-compete other groups under the prevailing conditions. Additionally, multivariate statistical analyses, Shannon's diversity, and evenness indices, principal component analysis, biplot and un-weighted-pair-group method with arithmetic averages dendrograms further confirmed that un-mined sites were distinctly different from the rehabilitated soils.

Bacterial and archaeal assemblages in sediments of a large shallow freshwater lake, Lake Taihu, as revealed by denaturing gradient gel electrophoresis

AIMS

To explore the association of microbial community structure with the development of eutrophication in a large shallow freshwater lake, Lake Taihu.

METHODS AND RESULTS

The bacterial and archaeal assemblages in sediments of different lake areas were analysed using denaturing gradient gel electrophoresis (DGGE) of amplified 16S rDNA fragments. The bacterial DGGE profiles showed that eutrophied sites, grass-bottom areas and relatively clean sites with a eutrophic (albeit dredged) site are three respective clusters. Fifty-one dominant bacterial DGGE bands were detected and 92 corresponding clones were sequenced, most of which were affiliated with bacterial phylotypes commonly found in freshwater ecosystems. Actinobacteria were detected in the centre of the lake and not at eutrophied sites whereas the opposite was found with respect to Verrucomicrobiales. Twenty-five dominant archaeal DGGE bands were detected and 31 corresponding clones were sequenced, most of which were affiliated with freshwater archaeal phylotypes.

CONCLUSIONS

The bacterial community structures in the sediments of different areas with similar water quality and situation tend to be similar in Taihu Lake.

SIGNIFICANCE AND IMPACT OF THE STUDY

This study may expand our knowledge on the relationship between the overall microbial assemblages and the development of eutrophication in the shallow freshwater lake.