Heterotrophic Populations Research Articles

Metabolic activities of marine ammonia-oxidizing archaea orchestrated by quorum sensing.

Ammonia-oxidizing archaea (AOA) play crucial roles in marine carbon and nitrogen cycles by fixing inorganic carbon and performing the initial step of nitrification. Evaluation of carbon and nitrogen metabolism popularly relies on functional genes such as amoA and accA. Increasing studies suggest that quorum sensing (QS) mainly studied in biofilms for bacteria may serve as a universal communication and regulatory mechanism among prokaryotes; however, this has yet to be demonstrated in marine planktonic archaea. To bridge this knowledge gap, we employed a combination of metabolic activity markers (amoA, accA, and grs) to elucidate the regulation of AOA-mediated nitrogen, carbon processes, and their interactions with the surrounding heterotrophic population. Through co-transcription investigations linking metabolic markers to potential key QS genes, we discovered that QS molecules could regulate AOA's carbon, nitrogen, and lipid metabolisms under different conditions. Interestingly, specific AOA ecotypes showed a preference for employing distinct QS systems and a distinct QS circuit involving a typical population. Overall, our data demonstrate that QS orchestrates nitrogen and carbon metabolism, including the exchange of organic metabolites between AOA and surrounding heterotrophic bacteria, which has been previously overlooked in marine AOA research.

Simultaneous nitrification and denitrification pattern in aerated moving-bed sequencing batch reactor: Choosing appropriate SRT for different COD/N ratios

ABSTRACT The effect of chemical oxygen demand (COD)/N ratio and sludge retention time (SRT) on the simultaneous nitrification and denitrification (SND) process in an aerated moving-bed sequencing batch reactor (A-MBSBR), for treating synthetic municipal wastewater, was studied. Three lab-scale reactors with SRTs of 5, 10, and 15 days were operated under COD/N ratios of 10 (phase 1) and 20 (phase 2). The high correlation coefficients between nitrification and denitrification efficiencies in both phases demonstrated that the denitrification efficiency in A-MBSBRs was strongly affected by nitrification efficiency (nitrate concentration). A high COD/N ratio of 20 in phase 2 provided suitable conditions for the increase and dominance of the population of heterotrophic bacteria over autotrophic nitrifiers, which led to weak nitrification (29.6–39.1%) and consequently weak denitrification (15.8–27.9%) in all reactors. In phase 2, increasing SRT from 5 to 15 days was beneficial for both nitrification and denitrification reactions. Therefore, the optimal SND efficiency in phase 2 was expected to be achieved under SRTs higher than 15 days. Under the COD/N ratio of 10 in phase 1, a better balance between the population of heterotrophs and autotrophs resulted in higher nitrification and denitrification efficiencies (44.4–62.7% and 26.3–42.8%, respectively). In phase 1, the highest and the lowest nitrification and denitrification efficiencies were obtained at SRTs of 10 and 5 days, respectively.

Salt pollution reduces turbidity, dissolved organic matter, and cyanobacteria in experimental vernal pool communities

Anthropogenic activities such as the over-application of road deicers are causing an increase in the concentration of salts in historically fresh waters. Experimental and field investigations demonstrate that freshwater salinization disrupts ecosystem functions and services, causing the death of freshwater organisms and changes to nutrient conditions. Wetland habitats are one system negatively affected by salt pollution, including ephemeral wetlands (vernal pools) that fill with salt-polluted water after snowmelt. In urbanized areas, the degradation of these ecosystems could result in irreversible ecological damage including reduced water quality and a reduction in biodiversity. To investigate the effects of freshwater salinization on vernal pool communities, we exposed soils from vernal pools to water containing no salt (control), or four concentrations of three salts standardized by chloride concentration (50 mg Cl− L−1, 100 mg Cl− L−1, 200 mg Cl− L−1, and 400 mg Cl− L−1; magnesium chloride, calcium chloride, and sodium chloride). The results of this experiment suggest that emerging zooplankton communities in vernal pools are sensitive to low concentrations of salt pollution, and that alternative salts such as magnesium chloride and calcium chloride are more toxic than sodium chloride. We did not find positive or negative changes in the abundance of eukaryotic phytoplankton but did find negative effects of salt on cyanobacteria abundance, possibly due to corresponding reductions in turbidity which might be needed as a fixation site for cyanobacteria to form heterocysts. Finally, we found that salt pollution likely caused flocculation of Dissolved Organic Matter (DOM), resulting in reduced concentrations of DOM which could alter the buffering capacity of freshwater systems, light attenuation, and the populations of planktonic heterotrophs.

Temporal dynamics of bacterial populations in recirculating aquaculture systems for sea urchin production

Introduction: Sea urchin aquaculture is a rising industry, and in consequence, there is a need to establish optimal culture parameters to ensure the health of the cultured animals.
 Objective: To evaluate the bacterial counts in the seawater of sea urchin (Arbacia dufresnii) aquaculture recirculating systems (RAS).
 Methods: The bacteriological water quality of two RAS containing sea urchins was determined. For approximately two months, weekly water samples were taken. The bacteriological quality was determined by counting total aerobic heterotrophic populations, lactic acid bacteria, enterobacterias and genus Vibrio. Physicochemical parameters were also measured.
 Results: There was no presence of disease or mortality. Enterobacteria and lactic acid bacteria were not detected from both RAS systems. The number of animals had an important effect on the observed difference in the count of total bacteria and Vibrio spp. In RAS 1 the maximum counts of total bacteria and Vibrio spp. were 2.8 x 105 ± 1.7 x 105 and 1.45 x 105 ± 3.6 x 104 UFC ml-1, respectively. In RAS 2 total bacteria and Vibrio spp. exhibited repetitive behavior over time influenced in part by water exchange and mainly by feeding. The results indicate that periodic water changes ensure a limited growth of bacterial strains as Vibrio and other bacteria.
 Conclusions: Our results suggests that the bacterial count levels recorded in this study can be used as a threshold or safety limit for Arbacia dufresnii aquaculture.

Phylogenetic and metabolic diversity of microbial communities performing anaerobic ammonium and methane oxidations under different nitrogen loadings

The microbial guild coupling anammox and nitrite/nitrate-dependent anaerobic methane oxidation (n-DAMO) is an innovative process to achieve energy-efficient nitrogen removal with the beneficial use of methane in biogas or in anaerobically treated wastewater. Here, metagenomics and metatranscriptomics were used to reveal the microbial ecology of two biofilm systems, which incorporate anammox and n-DAMO for high-level nitrogen removal in low-strength domestic sewage and high-strength sidestream wastewater, respectively. We find that different nitrogen loadings (i.e., 0.1 vs. 1.0 kg N/m3/d) lead to different combinations of anammox bacteria and anaerobic methanotrophs (“Candidatus Methanoperedens” and “Candidatus Methylomirabilis”), which play primary roles for carbon and nitrogen transformations therein. Despite methane being the only exogenous organic carbon supplied, heterotrophic populations (e.g., Verrucomicrobiota and Bacteroidota) co-exist and actively perform partial denitrification or dissimilatory nitrate reduction to ammonium (DNRA), likely using organic intermediates from the breakdown of methane and biomass as carbon sources. More importantly, two novel genomes belonging to “Ca. Methylomirabilis” are recovered, while one surprisingly expresses nitrate reductases, which we designate as “Ca. Methylomirabilis nitratireducens” representing its inferred capability in performing nitrate-dependent anaerobic methane oxidation. This finding not only suggests a previously neglected possibility of “Ca. Methylomirabilis” bacteria in performing methane-dependent nitrate reduction, and also challenges the previous understanding that the methane-dependent complete denitrification from nitrate to dinitrogen gas is carried out by the consortium of bacteria and archaea.

Biogeochemical niches and trophic plasticity of shallow and mesophotic corals recovering from mass bleaching

AbstractThe differential survival of corals and their recovery from oceanic thermal stress is related not only to coral bleaching susceptibility but also physiological plasticity including trophic strategy. We investigated post‐bleaching event recovery of three morphologically diverse, reef‐building coral species from shallow (10 m) and mesophotic (30 m) reefs across the Maldives archipelago. Trophic plasticity was evaluated by carbon and nitrogen contents and stable isotopes of coral hosts and their algal symbionts including isotopic niche position and size. Seawater temperatures recorded before, during, and after the mass coral bleaching event revealed significant thermal stress in both shallow and mesophotic reefs although cumulative warming appeared lower in mesophotic reefs (9.0 vs. 5.9 degree heating weeks, respectively). Ten months following thermal stress, increased nitrogen stable isotope (δ15N) values in all three coral host species without concurrent changes in water column δ15N indicated enhanced heterotrophic feeding during thermal stress and/or recovery. Host C:N decreased in all species post‐bleaching event while host carbon content (%C) decreased in shallow, more autotrophic populations of two species, suggesting prolonged stress. Host carbon stable isotope (δ13C) values were lower in mesophotic, more heterotrophic populations of two species compared to shallow counterparts. Biogeochemical and isotopic niches both showed different niche specialization among the three species. Consistent shifts in host isotopic niche positions support a conserved host response mechanism (heterotrophy) to oceanic thermal stress, but shallow and mesophotic corals still had not fully recovered almost one year after the bleaching event.

Micron-scale biogeography reveals conservative intra anammox bacteria spatial co-associations

Micron-scale resolution can help to reliably identify true taxon-taxon interactions in complex microbial communities. Despite widespread recognition of the critical role of metabolic interactions in anaerobic ammonium oxidation (anammox) system performance, no studies have examined microbial interactions at the micron-scale in anammox consortia. To fill this gap, we extensively sampled (totally 242 samples) the consortia of a lab-scale anammox reactor at different length scales, including bulk-scale (∼cm), macro-scale (300–500 µm) and micron-scale (70–100 µm). We firstly observed evident micron-scale heterogeneity in anammox consortia, with the relative abundance of anammox bacteria fluctuated greatly across individual clusters (2.0%–79.3%), indicating that the biotic interactions play a significant role in the assembly of anammox communities under well-controlled and well-mixed condition. Importantly, by mapping the spatial associations in anammox consortia at micron-scale, we demonstrated that the conserved co-associations for anammox bacteria were restricted to three different Brocadia species over time, and their co-associations with heterotrophs were random, implying that there was no statistically significant symbiotic interaction between anammox bacteria and other heterotrophic populations. Further metagenomic binning revealed that the quorum sensing with secondary messenger c-di-GMP potentially holding on the conservative metabolic cooperation among Brocadia species. These results shed new light on the social behavior of the anammox community. Overall, delineating of biological structures at micron-scale opens a new way of monitoring the microbial spatial structure and interactions, paving the way for improved community engineering of biotreatment systems.

Metagenomic Insights Into Competition Between Denitrification and Dissimilatory Nitrate Reduction to Ammonia Within One-Stage and Two-Stage Partial-Nitritation Anammox Bioreactor Configurations.

Anaerobic ammonia oxidizing bacteria (Anammox) are implemented in high-efficiency wastewater treatment systems operated in two general configurations; one-stage systems combine aerobic ammonia oxidizing bacteria (AOB) and Anammox within a single aerated reactor, whereas two-stage configurations separate these processes into discrete tanks. Within both configurations heterotrophic populations that perform denitrification or dissimilatory nitrate reduction to ammonia (DNRA) compete for carbon and nitrate or nitrite and can impact reactor performance because DNRA retains nitrogen in the system. Therefore, it is important to understand how selective pressures imposed by one-stage and two-stage reactor configurations impact the microbial community structure and associated nitrogen transforming functions. We performed 16S rRNA gene and metagenomic sequencing on different biomass fractions (granules, flocs, and suspended biomass) sampled from two facilities treating sludge dewatering centrate: a one-stage treatment facility (Chambers Creek, Tacoma, WA) and a two-stage system (Rotterdam, Netherlands). Similar microbial populations were identified across the different samples, but relative abundances differed between reactor configurations and biomass sources. Analysis of metagenome assembled genomes (MAGs) indicated different lifestyles for abundant heterotrophic populations. Acidobacteria, Bacteroidetes, and Chloroflexi MAGs had varying capacity for DNRA and denitrification. Acidobacteria MAGs possessed high numbers of glycosyl hydrolases and glycosyl transferases indicating a role in biomass degradation. Ignavibacteria and Phycosphaerae MAGs contributed to the greater relative abundance of DNRA associated nrf genes in the two-stage granules and contained genomic features suggesting a preference for an anoxic or microoxic niche. In the one-stage granules a MAG assigned to Burkholderiales accounted for much of the abundant denitrification genes and had genomic features, including the potential for autotrophic denitrification using reduced sulfur, that indicate an ability to adapt its physiology to varying redox conditions. Overall, the competition for carbon substrates between denitrifying and DNRA performing heterotrophs may be impacted by configuration specific selective pressures. In one-stage systems oxygen availability in the bulk liquid and the oxygen gradient within granules would provide a greater niche space for heterotrophic populations capable of utilizing both oxygen and nitrate or nitrite as terminal electron acceptors, compared to two-stage systems where a homogeneous anoxic environment would favor heterotrophic populations primarily adapted to anaerobic metabolism.

Metaproteomics, Heterotrophic Growth, and Distribution of Nitrosomonas europaea and Nitrobacter winogradskyi after Long-Term Operation of an Autotrophic Nitrifying Biofilm Reactor

Bioregenerative life support systems (BLSS) are currently in development to tackle low recovery efficiencies, high energy demands, as well as food, water, and oxygen production challenges through the regeneration of nutrients from waste streams. The MELiSSA pilot plant has been developed as a testbed for regenerative life support system bioreactor operation and characterization. As nitrogen is a vital resource in such systems, we studied the functional composition of a new packed-bed nitrifying bioreactor inoculated with a co-culture of Nitrosomonas europaea (ATCC 25978) and Nitrobacter winogradskyi (ATCC 25391). After 840 days of autotrophic continuous cultivation, the packed-bed was sampled at five vertical positions, each with three horizontal positions, and the biomass at each position was characterized via qPCR, 16S amplicon sequencing, and liquid chromatography tandem mass spectrometry. The total number of cells within the different sections fluctuated around 8.95 ± 5.10 × 107 cells/mL of beads. Based on 16S amplicons and protein content, N. europaea and N. winogradskyi constituted overall 44.07 ± 11.75% and 57.53 ± 12.04% of the nitrifying bioreactor, respectively, indicating the presence of a heterotrophic population that, even after such a long operation time, did not affect the nitrification function of the bioreactor. In addition, DNA-based abundance estimates showed that N. europaea was slightly more abundant than N. winogradskyi, whereas protein-based abundance estimates indicated a much higher abundance of N. europaea. This highlights that single-method approaches need to be carefully interpreted in terms of overall cell abundance and metabolic activity.

Ecological Interactions of Cyanobacteria and Heterotrophs Enhances the Robustness of Cyanobacterial Consortium for Carbon Sequestration.

Lack of robustness is a major barrier to foster a sustainable cyanobacterial biotechnology. Use of cyanobacterial consortium increases biodiversity, which provides functional redundancy and prevents invading species from disrupting the production ecosystem. Here we characterized a cyanobacterial consortium enriched from microbial mats of alkaline soda lakes in BC, Canada, at high pH and alkalinity. This consortium has been grown in open laboratory culture for 4 years without crashes. Using shotgun metagenomic sequencing, 29 heterotrophic metagenome-assembled-genomes (MAGs) were retrieved and were assigned to Bacteroidota, Alphaproteobacteria, Gammaproteobacteria, Verrucomicrobiota, Patescibacteria, Planctomycetota, and Archaea. In combination with metaproteomics, the overall stability of the consortium was determined under different cultivation conditions. Genome information from each heterotrophic population was investigated for six ecological niches created by cyanobacterial metabolism and one niche for phototrophy. Genome-resolved metaproteomics with stable isotope probing using 13C-bicarbonate (protein/SIP) showed tight coupling of carbon transfer from cyanobacteria to the heterotrophic populations, specially Wenzhouxiangella. The community structure was compared to a previously described consortium of a closely related cyanobacteria, which indicated that the results may be generalized. Productivity losses associated with heterotrophic metabolism were relatively small compared to other losses during photosynthesis.

Portioning of microbial waste into fish nutrition via frugal biofloc production: A sustainable paradigm for greening of environment

The goal of this study is to see whether biofloc technology (BFT) is suitable to grow Ompok bimaculatus (pabda) seeds. The experiment compared four levels of C/N ratio maintained using an exogenous carbon source, namely C/N10 (1.7 mL/L), 15 (6 mL/L), 20 (13.0 mL/L), and 25 (14.6 mL/L), to a control (0.0 mL/L) without any carbon addition. Pabda larvae (0.082 ± 0.001 g) were raised for 45 days in BFT 50 L glass aquaria. The effects of BFT with different C/N ratios on system water & floc quality, as well as on animal performance, feed utilization, and flesh quality, were studied. In comparison to the control, the results showed that BFT could effectively manage nitrogenous waste in the system. The BFT group had better nitrogen retention in stock biomass, with C/N20 (40.34%) having the best performance. Factor analysis revealed the dominance of the heterotrophic population in the system. The floc volume increased as the C/N ratio increased, however the size decreased. The level of floc protein decreased (p < 0.05) as the C/N ratio increased. BFT groups outperformed control groups in terms of growth, survival, and condition factor (p < 0.05), with C/N20 performing best. In addition, C/N20 noted a significant (p < 0.05) difference in feed conversion ratio (FCR) and protein efficiency ratio (PER) as compared to control. In the liver, gut, and muscle tissues, digestive enzymes such as amylase, lipase, and protease were higher in BFT, compared to control. Gut morphology was better in BFT groups (p < 0.05), with C/N20 showing increased height, width, and absorptive area of microvilli. The overall conclusion of this study is that varying C/N in the BFT system has an impact on system water quality, animal performance, feed utilization, floc characteristics, digestive function, and gut morphology. This research explains on how to use BFT as a long-term solution for in-situ waste conversion to reduce effluent load for pabda seed production. The study suggested a way not only for effective utilization of nutrient-enriched biofloc as nutritious feed supplements, but also paved the way for water conservation along with the safe conversion of microbial biofloc into fish nutrition for facilitating a clean environment.

Comparative Metagenomic Analysis of Two Hot Springs From Ourense (Northwestern Spain) and Others Worldwide.

With their circumneutral pH and their moderate temperature (66 and 68°C, respectively), As Burgas and Muiño da Veiga are two important human-use hot springs, previously studied with traditional culture methods, but never explored with a metagenomic approach. In the present study, we have performed metagenomic sequence-based analyses to compare the taxonomic composition and functional potential of these hot springs. Proteobacteria, Deinococcus-Thermus, Firmicutes, Nitrospirae, and Aquificae are the dominant phyla in both geothermal springs, but there is a significant difference in the abundance of these phyla between As Burgas and Muiño da Veiga. Phylum Proteobacteria dominates As Burgas ecosystem while Aquificae is the most abundant phylum in Muiño da Veiga. Taxonomic and functional analyses reveal that the variability in water geochemistry might be shaping the differences in the microbial communities inhabiting these geothermal springs. The content in organic compounds of As Burgas water promotes the presence of heterotrophic populations of the genera Acidovorax and Thermus, whereas the sulfate-rich water of Muiño da Veiga favors the co-dominance of genera Sulfurihydrogenibium and Thermodesulfovibrio. Differences in ammonia concentration exert a selective pressure toward the growth of nitrogen-fixing bacteria such as Thermodesulfovibrio in Muiño da Veiga. Temperature and pH are two important factors shaping hot springs microbial communities as was determined by comparative analysis with other thermal springs.

Heterotrophic bacterial diazotrophs are more abundant than their cyanobacterial counterparts in metagenomes covering most of the sunlit ocean.

Biological nitrogen fixation contributes significantly to marine primary productivity. The current view depicts few cyanobacterial diazotrophs as the main marine nitrogen fixers. Here, we used 891 Tara Oceans metagenomes derived from surface waters of five oceans and two seas to generate a manually curated genomic database corresponding to free-living, filamentous, colony-forming, particle-attached, and symbiotic bacterial and archaeal populations. The database provides the genomic content of eight cyanobacterial diazotrophs including a newly discovered population related to known heterocystous symbionts of diatoms, as well as 40 heterotrophic bacterial diazotrophs that considerably expand the known diversity of abundant marine nitrogen fixers. These 48 populations encapsulate 92% of metagenomic signal for known nifH genes in the sunlit ocean, suggesting that the genomic characterization of the most abundant marine diazotrophs may be nearing completion. Newly identified heterotrophic bacterial diazotrophs are widespread, express their nifH genes in situ, and also occur in large planktonic size fractions where they might form aggregates that provide the low-oxygen microenvironments required for nitrogen fixation. Critically, we found heterotrophic bacterial diazotrophs to be more abundant than cyanobacterial diazotrophs in most metagenomes from the open oceans and seas, emphasizing the importance of a wide range of heterotrophic populations in the marine nitrogen balance.

Phytoplankton exudates and lysates support distinct microbial consortia with specialized metabolic and ecophysiological traits

Blooms of marine phytoplankton fix complex pools of dissolved organic matter (DOM) that are thought to be partitioned among hundreds of heterotrophic microbes at the base of the food web. While the relationship between microbial consumers and phytoplankton DOM is a key component of marine carbon cycling, microbial loop metabolism is largely understood from model organisms and substrates. Here, we took an untargeted approach to measure and analyze partitioning of four distinct phytoplankton-derived DOM pools among heterotrophic populations in a natural microbial community using a combination of ecogenomics, stable isotope probing (SIP), and proteomics. Each 13C-labeled exudate or lysate from a diatom or a picocyanobacterium was preferentially assimilated by different heterotrophic taxa with specialized metabolic and physiological adaptations. Bacteroidetes populations, with their unique high-molecular-weight transporters, were superior competitors for DOM derived from diatom cell lysis, rapidly increasing growth rates and ribosomal protein expression to produce new relatively high C:N biomass. Proteobacteria responses varied, with relatively low levels of assimilation by Gammaproteobacteria populations, while copiotrophic Alphaproteobacteria such as the Roseobacter clade, with their diverse array of ABC- and TRAP-type transporters to scavenge monomers and nitrogen-rich metabolites, accounted for nearly all cyanobacteria exudate assimilation and produced new relatively low C:N biomass. Carbon assimilation rates calculated from SIP data show that exudate and lysate from two common marine phytoplankton are being used by taxonomically distinct sets of heterotrophic populations with unique metabolic adaptations, providing a deeper mechanistic understanding of consumer succession and carbon use during marine bloom events.

Short term response of plankton community to nutrient enrichment in central eastern Arabian Sea: Elucidation through mesocosm experiments

Oligotrophic waters (OW), generally favour longer food chain facilitated by the microbial loop. In such ecosystems, physical mixing (e.g. upwelling, and winter convection) inject nutrients and propagules from subsurface to the photic zone. Such events are expected to alter the food chain through shifts in the plankton community. Mesocosm experiments were carried out to evaluate the influence of nutrient enrichment from the deep (100–150 m) on the surface plankton community for the first time in the Arabian Sea, through custom-designed enclosures in OW of the central-eastern Arabian Sea (CEAS). Surface water was characterized by low nutrients and phytoplankton biomass (chlorophyll-a of <0.2 μg m−3) and upon nutrient enrichment yielded differing response. Higher abundance of picophytoplankton, bacteria and protists was noticed at a depth of ~100 m than at surface. The inoculation of such a population to the surface, resulted in a significant enhancement of autotrophic (picophytoplankton) and heterotrophic (bacteria and protists) populations. However, significant changes in the abundance of larger plankton was not evident till three days of incubation. Even though autotrophic picophytoplankton responded positively, a distinct increase in chlorophyll-a was not evident. This study points out that the lack of sufficient viable microphytoplankton propagules, neither at the surface nor at the depth (inoculum) are the possible reasons for the lack of their distinct positive response. These experiments suggest the dominance of microbial community response to physical mixing in the OW regions of the Arabian Sea and the importance of propagule diversity. The insights from this experiment will serve as a precursor for appropriate modifications in ocean modelling and forecasting studies and help in building global environmental management tools.

Heterotrophic enzymatic biotransformations of organic micropollutants in activated sludge.

While heterotrophic microorganisms constitute the major fraction of activated sludge biomass, the role of heterotrophs in the biotransformation of organic micropollutants (OMPs) has not been fully elucidated. Yet, such knowledge is essential, particularly when conceiving novel wastewater treatment plants based on a two-stage process including an A-stage under heterotrophic conditions and a B-stage based on anammox activity. Biotransformation of OMPs in activated sludge is thought to mostly occur cometabolically thanks to the action of low specificity enzymes involved in the metabolism of the primary substrates. For a better understanding of the process, it is important to determine such enzymatic activities and the underlying mechanisms involved in OMPs biotransformation. This task has proven to be difficult due to the lack of information about the enzymatic processes and the complexity of the biological systems present in activated sludge. In this paper, a continuous aerobic heterotrophic reactor following 20 OMPs at environmental concentrations was operated to (i) assess the potential of heterotrophs during the cometabolic biotransformation of OMPs, (ii) identify biotransformation reactions catalyzed by aerobic heterotrophs and (iii) predict possible heterotrophic enzymatic activities responsible for such biotransformations. Contradicting previous reports on the dominant role of nitrifiers in OMPs removal during activated sludge treatment, the heterotrophic population proved its capacity to biotransform the OMPs to extents equivalent to reported values in nitrifying activated sludge plants. Besides, 12 transformation products potentially formed through the activity of several enzymes present in heterotrophs, including monooxygenases, dioxygenases, hydrolases and transferases, were identified.

Determination of ED50 in a Calcareous Soil Contaminated with Different Concentrations of Ni

Background and Objectives: Soil microbial properties such as biomass, microbial respiration and nitrogen mineralization can be used as indicators to show the stress caused by heavy metal pollution on soil quality. The aim of this study was the measurement soil microbial activity to evaluate the effect of soil Ni contamination on soil quality and determination of ecological dose 50 (ED50). Method: This study was conducted as a factorial experiment in year 2016 based on a randomized completely design with three replications. The experiment factors including Ni concentration in six levels (0, 50, 100, 150, 300 and 600 mg Ni kg-1) and two incubation times (15 and 60 days). Soils sample was spiked uniformly with different concentrations of NiCl2. Microbial respiration, microbial biomass carbon, heterotrophic population and metabolic quotient were measured after incubation times of 15 and 60 days, then according to the results, ED50 was determined by using the dose-response curve. Findings: Soil Nickel contamination on the indicator was significantly effective at P<0.01 level. Heterotrophic population, respiration and microbial carbon biomass decreased significantly (P<0.01) compared to control by increasing the Ni concentration and incubation times, whereas the increase of Ni concentration and incubation times were not significantly affected on metabolic quotient. The minimum amount of microbial respiration, microbial biomass carbon, and the heterotrophic population was observed at the end of incubation times and 600 mg Ni kg-1 with 77.07, 75.72 and 99.99% decrement compared to the control, respectively. ED50 value (mg/kg soil) of microbial respiration, microbial biomass carbon, and heterotroph population increased from 77.55, 78.63, 81.34 to 97.84, 111.04 and 84.67 respectively, with increased incubation time. Discussion and Conclusion: The soil contaminated with Nickel acutely decreased the biological activity of soil and the ecological dose increased with increasing the incubation time, suggesting that toxicity of Ni to soil microbial activity was decreased with increased incubation time. Ni concentration of 100 mgNikg-1 soil can be considered as the critical range of Ni for soil quality at which negative effect was observed.

Genomic and enzymatic evidence of acetogenesis by anaerobic methanotrophic archaea

Anaerobic oxidation of methane (AOM) mediated by anaerobic methanotrophic archaea (ANME) is the primary process that provides energy to cold seep ecosystems by converting methane into inorganic carbon. Notably, cold seep ecosystems are dominated by highly divergent heterotrophic microorganisms. The role of the AOM process in supporting heterotrophic population remains unknown. We investigate the acetogenic capacity of ANME-2a in a simulated cold seep ecosystem using high-pressure biotechnology, where both AOM activity and acetate production are detected. The production of acetate from methane is confirmed by isotope-labeling experiments. A complete archaeal acetogenesis pathway is identified in the ANME-2a genome, and apparent acetogenic activity of the key enzymes ADP-forming acetate-CoA ligase and acetyl-CoA synthetase is demonstrated. Here, we propose a modified model of carbon cycling in cold seeps: during AOM process, methane can be converted into organic carbon, such as acetate, which further fuels the heterotrophic community in the ecosystem.

Psychrotrophic violacein-producing bacteria isolated from Lake Winnipeg, Canada

Violet and purple bacterial pigmentations are uncommon when considering strict aerobes. Here we report discovery of two novel isolates, P102 and P117 from the freshwater Lake Winnipeg, each with violet to deep purple colony colouration. The relationship between pigment production and growth was investigated under different conditions, including a variety of carbon sources, pH, and temperatures. The violet compounds were purified using polar organic solvents, and then structurally characterized via mass spectrometry and nuclear magnetic resonance to be violacein and deoxyviolacein. Strain P117 produced higher concentrations of the darker pigment deoxyviolacein, which resulted in a deeper hue of violet than in cultures of P102. Strain P102, synthesized violacein maximally in liquid rich organic medium at pH 8 and 20 °C, and had 99.3% sequence similarity to the 16S rDNA from Janthinobacterium lividum. Strain P117, related to Massilia violaceinigra sharing 99.2% 16S rDNA sequence similarity, also produced violacein at similar optimal conditions, but developed higher concentrations of pigment at 15 °C. Culture-based methods found that violacein producers composed 0.001% or 0.023% CFU of environmental heterotrophic populations using BG-11 and potato-based media, respectively. Culture-independent high-throughput ribosomal 16S V4 sequencing of environmental DNA was used to detect Gram-negative species known for their production of violacein. Of all bacterial and archaeal sequences present during the fall in littoral waters and sediment of Lake Winnipeg, 5.5% and 6.3%, respectively, belonged to species that have similar pigment, demonstrating the scarcity of violacein producers in this aquatic freshwater system.

Partitioning of total soil respiration into root, rhizosphere and basal-soil CO2 fluxes in contrasting rice production systems

Soil respiration contributes significantly to ecosystem respiration and is vital in the context of climate change research. In a season-long experiment we studied total soil respiration (TSR) and its partitioning into root respiration, rhizospheric respiration (RhR) and basal-soil respiration in four contrasting rice production systems: irrigated lowland (IL) (cv. Gayatri); organic nutrient managed irrigated lowland (OIL) (cv. Geetanjali); system of rice intensification (SRI) (cv. Swarna); and aerobic rice system (Aerobic) (cv. APO). We considered TSR to be the sum of root respiration, RhR and basal-soil respiration. Irrespective of the rice production system, TSR was higher at panicle initiation stage. Considering all four systems, the RhR contributed the most (59–83%) and basal-soil respiration the least (10–19%) to the TSR. Mean RhR showed the trend of Aerobic &amp;gt; SRI &amp;gt; IL &amp;gt; OIL across the growing seasons and indicated higher rhizosphere activities in the aerobic system. Mean root respiration showed a trend of IL &amp;gt; OIL &amp;gt; SRI &amp;gt; Aerobic and mean basal-soil respiration had SRI &amp;gt; IL &amp;gt; OIL &amp;gt; Aerobic. Soil labile carbon pools and heterotrophic populations were higher in OIL and dehydrogenase activity was higher in SRI. Microbial biomass carbon, readily mineralisable carbon, dehydrogenase activity and the heterotroph population showed positive correlations with RhR. Hence, regulation of RhR is crucial and can be achieved through rhizosphere modifications linked with labile carbon pools and soil enzymatic activities by plant physiological modification or through soil carbon stabilisation.