Carbon source shaped microbial ecology, metabolism and performance in denitrification systems

The limited information on microbial interactions and metabolic patterns in denitrification systems, especially those fed with different carbon sources, has hindered the establishment of ecological linkages between microscale connections and macroscopic reactor performance. In this work, denitrification performance, metabolic patterns, and ecological structure were investigated in parallel well-controlled bioreactors with four representative carbon sources, i.e., methanol, glycerol, acetate, and glucose. After long-term acclimation, significant differences were observed among the four bioreactors in terms of denitrification rates, organic utilization, and heterotrophic bacterial yields. Different carbon sources induced the succession of denitrifying microbiota toward different ecological structures and exhibited distinct metabolic patterns. Methanol-fed reactors showed distinctive microbial carbon utilization pathways and a more intricate microbial interaction network, leading to significant variations in organic utilization and metabolite production compared to other carbon sources. Three keystone taxa belonging to the Verrucomicrobiota phylum, SJA-15 order and the Kineosphaera genus appeared as network hubs in the methanol, glycerol, and acetate-fed systems, playing essential roles in their ecological functions. Several highly connected species were also identified within the glucose-fed system. The close relationship between microbial metabolites, ecological structures, and system performances suggests that this complex network relationship may greatly contribute to the efficient operation of bioreactors.

Co-occurrence pattern of ARGs and N-functional genes in the aerobic composting system with initial elevated temperature

Animal manure is known to harbor antibiotic resistance genes (ARGs). Aerobic composting is a prevalent cost-effective and sustainable method to treat animal waste. However, the effect of initially elevated temperature on antibiotic resistome during the composting process is unclear. In this study composting was subjected to initial external heating (EHC) for a period of 5 days compared to conventional composting (CC). After composting ARGs abundance was significantly reduced by 2.43 log in EHC and 1.95 log in CC. Mobile genetic elements (MGEs) also exhibited a reduction of 1.95 log in EHC and 1.49 log in CC. However, during the cooling phase, the genes resisting macrolide lincosamide and streptogramin B (MLSB) rebounded by 0.04 log in CC. The potential human pathogenic bacteria Pseudomonas (41.5-61.5%) and Actinobacteria (98.4-98.8%) were significantly reduced in both treatments and the bulk of targeted antibiotics were eliminated by 80.74% in EHC and 68.98% in CC. ARGs and N-functional genes (NFGs), mainly denitrification genes, were carried by the same microbial species, such as Corynebacterium sp. and Bacillus sp., of the dominant phylum. Redundancy analysis (RDA) revealed that CC microbial communities played a key role in the enrichment of ARGs while in EHC the variation of ARGs was attributed to the composting temperature. The number of high-risk ARGs was also lower in EHC (4) compared with CC (6) on day 30. These results provide insight into the effects of an initially enhanced temperature on ARGs removal and the relationship between ARGs and NFGs during the composting process.

Ammonium Reactive Migration Process and Functional Bacteria Response along Lateral Runoff Path under Groundwater Exploitation

In order to elucidate the importance of biogeochemical interactions between NH4+ and aquifer media in groundwater runoff paths, a dynamic monitoring section in the riverbank zone, which is most sensitive to environmental characteristics and perpendicular to the flow direction of the Songhua River in northeastern China, was selected for field experiments in this study. The results indicated that the NH4+ concentration decreased gradually along the groundwater runoff path under exploitation conditions. The NH4+ concentrations of J1, J2, and J3 decreased by 8%, 18%, and 22%, respectively, as compared to the starting concentration of 1.3 mg/L. Adsorption of NH4+ by aquifer media at different depths is a monolayer adsorption process in accordance with pseudo-second-order kinetic equation. The maximum reduction of NH4+ from the aquifer media from top to bottom was 76%, 67%, 56%, and 42%, respectively. The function and activity of dominant functional bacteria have characteristics of coevolution with the NH4+ transformation process. The main genera in the fluctuation zone are Pseudomonas (8.83%) and Acinetobacter (4.37%), which mainly transform NH4+ by heterotrophic nitrification–aerobic denitrification (HN–AD). The main genera in the saturated zone are Flavobacterium (32.60%) and Sphingobium (3.54%), which mainly transform NH4+ by anaerobic denitrification. The spatial variations of species and abundance for NH4+ transformation functional bacteria decrease by 2.74% and 3.47%, respectively, along groundwater runoff paths. In the vertical and horizontal directions of groundwater runoff, the percentage of adsorption in NH4+ transformation gradually decreased and the percentage of biotransformation gradually increased. The adsorption processes in the O2/NO3− reduction, Fe/Mn reduction, and SO42− reduction zones were 20.7%, 3.6%, and 1.0%, respectively. The corresponding proportions of the biotransformation process were 79.3%, 96.4%, and 99.0%. This research is critical for elucidating the bio-geochemical interaction between NH4+ and aquifer media along the course of groundwater runoff in order to offer a scientific basis for the prevention and management of groundwater nitrogen pollution.

Accelerating Microbial Activity of Soil Aquifer Treatment by Hydrogen Peroxide

Soil aquifer treatment (SAT), as a gravity-based wastewater reuse process, is limited by oxygen availability to the microbial community in the soil. Using oxygen from enzymatic degradation of H2O2 to generate hyper-oxygen conditions can exceed solubility limitations associated with aeration, but little is known about the effect of hyper-oxygen conditions on the microbial community and the dominant bio-reactions. This study examined the impact of H2O2 addition on the community structure and process performance, along with SAT depth. Overall, two soil columns were incrementally fed synthetic secondary effluents to simulate infiltration through SAT. The experimental column received 14 mg/L hydrogen peroxide to double the level of natural oxygen available. The microbial kinetics of nitrifiers and heterotrophs were evaluated. We found that all of the H2O2 was degraded within the top 10 cm of the column, accompanied by a higher removal of COD (23 ± 0.25%) and ammonia (31 ± 3%) in comparison to the reference column. Higher nitrogen removal (23 ± 0.04%) was obtained for the whole process using H2O2. Analysis of nitrifiers indicated that ammonia-oxidizing bacteria were most influenced, obtaining higher concentration and abundance when exposed to H2O2. DNA sequencing analysis of samples exposed to H2O2 revealed significant community structure and diversity differences among heterotrophs. This study shows that not only aerobic, but also anoxic, microbial activity and process performance in a SAT system could be accelerated in existing infrastructure with H2O2, which could significantly decrease the associated environmental footprint.

Genomic structure predicts metabolite dynamics in microbial communities

The metabolic activities of microbial communities play a defining role in the evolution and persistence of life on Earth, driving redox reactions that give rise to global biogeochemical cycles. Community metabolism emerges from a hierarchy of processes, including gene expression, ecological interactions, and environmental factors. In wild communities, gene content is correlated with environmental context, but predicting metabolite dynamics from genomes remains elusive. Here, we show, for the process of denitrification, that metabolite dynamics of a community are predictable from the genes each member of the community possesses. A simple linear regression reveals a sparse and generalizable mapping from gene content to metabolite dynamics for genomically diverse bacteria. A consumer-resource model correctly predicts community metabolite dynamics from single-strain phenotypes. Our results demonstrate that the conserved impacts of metabolic genes can predict community metabolite dynamics, enabling the prediction of metabolite dynamics from metagenomes, designing denitrifying communities, and discovering how genome evolution impacts metabolism.

Moso Bamboo Invasion Reshapes Community Structure of Denitrifying Bacteria in Rhizosphere of Alsophila spinulosa

The uncontrolled invasion of moso bamboo (Phyllostachys pubescens) dramatically alters soil nitrogen cycling and destroys the natural habitat of Alsophila spinulosa. Nevertheless, no clear evidence points out the role of denitrifying bacteria in the invasion of bamboo into the habitat of A. spinulosa. In the present study, we found that low (importance value 0.0008), moderate (0.6551), and high (0.9326) bamboo invasions dramatically altered the underground root biomass of both P. pubescens and A. spinulosa. The root biomass of A. spinulosa was maximal at moderate invasion, indicating that intermediate disturbance might contribute to the growth and survival of the colonized plant. Successful bamboo invasion significantly increased rhizospheric soil available nitrogen content of A. spinulosa, coupled with elevated denitrifying bacterial abundance and diversity. Shewanella, Chitinophaga, and Achromobacter were the primary genera in the three invasions, whereas high bamboo invasion harbored more denitrifying bacteria and higher abundance than moderate and low invasions. Further correlation analysis found that most soil denitrifying bacteria were positively correlated with soil organic matter and available nitrogen but negatively correlated with pH and water content. In addition, our findings illustrated that two denitrifying bacteria, Chitinophaga and Sorangium, might be essential indicators for evaluating the effects of bamboo invasion on the growth of A. spinulosa. Collectively, this study found that moso bamboo invasion could change the nitrogen cycling of colonized habitats through alterations of denitrifying bacteria and provided valuable perspectives for profound recognizing the invasive impacts and mechanisms of bamboo expansion.

Role of heterotrophic nitrifiers and aerobic denitrifiers in simultaneous nitrification and denitrification process: A non-conventional nitrogen removal pathway in wastewater treatment

Bacterial species capable of performing both nitrification and denitrification in a single vessel under similar conditions have gained significance in the wastewater treatment scenario considering their unique character of performing the above reactions under heterotrophic and aerobic conditions respectively. Such a novel strategy often referred to as simultaneous nitrification and denitrification (SND) has a tremendous potential in dealing with various wastewaters having low C:N content, considering that the process needs very little or no external carbon source and oxygen supply thus adding to its cost-effective and environmentally friendly nature. Though like other microorganisms, heterotrophic nitrifiers and aerobic denitrifiers convert inorganic or organic nitrogen-containing substances into harmless dinitrogen gas in the wastewater, their ecophysiological role in the global nitrogen cycle is still not yet fully understood. Attempts to highlight the role played by the heterotrophic nitrifiers and aerobic denitrifiers in dealing with nitrogen pollution under various environmental operating conditions will help in developing a mechanistic understanding of the SND process to address the issues faced by the traditional methods of aerobic autotrophic nitrification-anaerobic heterotrophic denitrification.

Long-Term Fertilization Shapes the Putative Electrotrophic Microbial Community in Paddy Soils Revealed by Microbial Electrosynthesis Systems

Electrotrophs play an important role in biogeochemical cycles, but the effects of long-term fertilization on electrotrophic communities in paddy soils remain unclear. Here, we explored the responses of electrotrophic communities in paddy soil-based microcosms to different long-term fertilization practices using microbial electrosynthesis systems (MESs), high-throughput quantitative PCR, and 16s rRNA gene-based Illumina sequencing techniques. Compared to the case in the unfertilized soil (CK), applications of only manure (M); only chemical nitrogen, phosphorous, and potassium fertilizers (NPK); and M plus NPK (MNPK) clearly changed the electrotrophic bacterial community structure. The Streptomyces genus of the Actinobacteria phylum was the dominant electrotroph in the CK, M, and MNPK soils. The latter two soils also favored Truepera of Deinococcus-Thermus or Arenimonas and Thioalkalispira of Proteobacteria. Furthermore, Pseudomonas of Proteobacteria and Bacillus of Firmicutes were major electrotrophs in the NPK soil. These electrotrophs consumed biocathodic currents coupled with nitrate reduction and recovered 18-38% of electrons via dissimilatory nitrate reduction to ammonium (DNRA). The increased abundances of the nrfA gene for DNRA induced by electrical potential further supported that the electrotrophs enhanced DNRA for all soils. These expand our knowledge about the diversity of electrotrophs and their roles in N cycle in paddy soils and highlight the importance of fertilization in shaping electrotrophic communities.

Nitrate Respiration in Thermus thermophilus NAR1: from Horizontal Gene Transfer to Internal Evolution

Genes coding for enzymes of the denitrification pathway appear randomly distributed among isolates of the ancestral genus Thermus, but only in few strains of the species Thermus thermophilus has the pathway been studied to a certain detail. Here, we review the enzymes involved in this pathway present in T. thermophilus NAR1, a strain extensively employed as a model for nitrate respiration, in the light of its full sequence recently assembled through a combination of PacBio and Illumina technologies in order to counteract the systematic errors introduced by the former technique. The genome of this strain is divided in four replicons, a chromosome of 2,021,843 bp, two megaplasmids of 370,865 and 77,135 bp and a small plasmid of 9799 pb. Nitrate respiration is encoded in the largest megaplasmid, pTTHNP4, within a region that includes operons for O₂ and nitrate sensory systems, a nitrate reductase, nitrate and nitrite transporters and a nitrate specific NADH dehydrogenase, in addition to multiple insertion sequences (IS), suggesting its mobility-prone nature. Despite nitrite is the final product of nitrate respiration in this strain, the megaplasmid encodes two putative nitrite reductases of the cd1 and Cu-containing types, apparently inactivated by IS. No nitric oxide reductase genes have been found within this region, although the NorR sensory gene, needed for its expression, is found near the inactive nitrite respiration system. These data clearly support that partial denitrification in this strain is the consequence of recent deletions and IS insertions in genes involved in nitrite respiration. Based on these data, the capability of this strain to transfer or acquire denitrification clusters by horizontal gene transfer is discussed.

Niche differentiation of denitrifying anaerobic methane oxidizing bacteria and archaea leads to effective methane filtration in a Tibetan alpine wetland

Denitrifying anaerobic methane oxidation (DAMO) is a vital methane sink in wetlands. However, the interactions and niche partitioning of DAMO bacteria and archaea in freshwater wetland soils, in addition to the interactions among microorganisms that couple methane and nitrogen cycling is still unclear, despite that these factors may govern the fate of methane and nitrogen in wetlands. Here, we evaluated the vertical distribution of DAMO bacteria and archaea in soil layers along with the potential interactions among populations in the methane-coupled nitrogen cycling microbial community of Tibetan freshwater wetlands. A combination of molecular biology, stable isotope tracer technology, and microbial bioinformatics was used to evaluate these interrelated dynamics. The abundances and potential methane oxidation rates indicated that DAMO bacteria and archaea differentially occupy surface and subsurface soil layers, respectively. The inferred interactions between DAMO bacteria and nitrogen cycling microorganisms within their communities are complex, DAMO bacteria apparently achieve an advantage in the highly competitive environment of surface soils layers and occupy a specific niche in those environments. Conversely, the apparent relationships between DAMO archaea and nitrogen cycling microorganisms are relatively simple, wherein high levels of cooperation are inferred between DAMO archaea and nitrate-producing organisms in subsurface soils layers. These results suggest that the vertical distribution patterns of DAMO bacteria and archaea enable them to play significant roles in the methane oxidation activity of different soil layers and collectively form an effective methane filtration consortium.

Hierarchical detection of diverse Clade II (atypical) nosZ genes using new primer sets for classical- and multiplex PCR array applications

The reduction of nitrous oxide (N₂O) to N₂ represents the key terminal step in canonical denitrification. Nitrous oxide reductase (NosZ), the enzyme associated with this biological step, however, is not always affiliated with denitrifying microorganisms. Such organisms were shown recently to possess a Clade II (atypical) nosZ gene, in contrast to Clade I (typical) nosZ harbored in more commonly studied denitrifiers. Subsequent phylogenetic analyses have shown that Clade II NosZ are affiliated with a much broader diversity of microorganisms than those with Clade I NosZ, the former including both non-denitrifiers and denitrifiers. Most studies attempting to characterize the nosZ gene diversity using DNA-based PCR approaches have only focused on Clade I nosZ, despite recent metagenomic sequencing studies that have demonstrated the dominance of Clade II nosZ genes in many ecosystems, particularly soil. As a result, these studies have greatly underestimated the genetic potential for N₂O reduction present in ecosystems. Because the high diversity of Clade II NosZ makes it impossible to design a universal primer set that would effectively amplify all nosZ genes in this clade, we developed a suite of primer sets to specifically target seven of ten designated subclades of Clade II nosZ genes. The new primer sets yield suitable product sizes for paired end amplicon sequencing and qPCR, demonstrated here in their use for both conventional single-reaction and multiplex array platforms. In addition, we show the utility of these primers for detecting nosZ gene transcripts from mRNA extracted from soil.

Exposure to microplastics lowers arsenic accumulation and alters gut bacterial communities of earthworm Metaphire californica

Ubiquitous contamination of microplastics and arsenic in soil ecosystems can induce many health issues to nontarget soil organisms, and will also cause many potential threats to the gut bacterial communities of soil fauna. However, the changes in the gut bacterial communities of soil fauna after exposure to both microplastics and arsenic remain unknown. In this study, the toxicity and effects on the gut microbiota of earthworm Metaphire californica caused by the combined exposure of microplastics and arsenic were examined by using arsenic species analysis and high throughput sequencing of gut microbiota. Results showed that total arsenic and arsenic species in the earthworm gut and body tissues after exposure to combination of microplastics with arsenate (As(V)) were significantly different from that treated with As(V) alone. Microplastics lessened the accumulation of total arsenic and the transformation rate of As(V) to arsenite (As(III)). Microplastics alleviated the effect of arsenic on the gut microbiota possibly via adsorbing/binding As(V) and lowering arsenic bioavailability, thus prevented the reduction of As(V) and accumulation of total arsenic in the gut which resulted in a lower toxicity on the earthworm. The study broadens our understanding of the ecotoxicity of microplastics with other pollutants on the soil animals and on their gut microbiota.

Enhanced functionalisation of major facilitator superfamily transporters via fusion of C-terminal protein domains is both extensive and varied in bacteria

The evolution of gene fusions that result in covalently linked protein domains is widespread in bacteria, where spatially coupling domain functionalities can have functional advantages in vivo. Fusions to integral membrane proteins are less widely studied but could provide routes to enhance membrane function in synthetic biology. We studied the major facilitator superfamily (MFS), as the largest family of transporter proteins in bacteria, to examine the extent and nature of fusions to these proteins. A remarkably diverse variety of fusions are identified and the 8 most abundant examples are described, including additional enzymatic domains and a range of sensory and regulatory domains, many not previously described. Significantly, these fusions are found almost exclusively as C-terminal fusions, revealing that the usually cytoplasmic C-terminal end of MFS protein would the permissive end for engineering synthetic fusions to other cytoplasmic proteins.

Exploration of deep terrestrial subsurface microbiome in Late Cretaceous Deccan traps and underlying Archean basement, India

Scientific deep drilling at Koyna, western India provides a unique opportunity to explore microbial life within deep biosphere hosted by ~65 Myr old Deccan basalt and Archaean granitic basement. Characteristic low organic carbon content, mafic/felsic nature but distinct trend in sulfate and nitrate concentrations demarcates the basaltic and granitic zones as distinct ecological habitats. Quantitative PCR indicates a depth independent distribution of microorganisms predominated by bacteria. Abundance of dsrB and mcrA genes are relatively higher (at least one order of magnitude) in basalt compared to granite. Bacterial communities are dominated by Alpha-, Beta-, Gammaproteobacteria, Actinobacteria and Firmicutes, whereas Euryarchaeota is the major archaeal group. Strong correlation among the abundance of autotrophic and heterotrophic taxa is noted. Bacteria known for nitrite, sulfur and hydrogen oxidation represent the autotrophs. Fermentative, nitrate/sulfate reducing and methane metabolising microorganisms represent the heterotrophs. Lack of shared operational taxonomic units and distinct clustering of major taxa indicate possible community isolation. Shotgun metagenomics corroborate that chemolithoautotrophic assimilation of carbon coupled with fermentation and anaerobic respiration drive this deep biosphere. This first report on the geomicrobiology of the subsurface of Deccan traps provides an unprecedented opportunity to understand microbial composition and function in the terrestrial, igneous rock-hosted, deep biosphere.

Stability of continuous and fed batch sequential anaerobic-anoxic-aerobic moving bed bioreactor systems at phenol shock load application

The stability of two sequential moving bed bioreactor systems operated in anaerobic-anoxic-aerobic continuous moving bed bioreactor (CMBR: R1-R2-R3) and semi-continuous fed batch moving bed bioreactor (FMBR: B1-B2-B3) modes was assessed for phenol shock load (PSL) applications in the presence of thiocyanate and ammonia. Both the systems were exposed to 3000 mg phenol/L (PSL-I) and 3500 mg phenol/L (PSL-II) for 3 days each from initial 2500 mg phenol/L without any intermediate concentration at 6 days HRT (hydraulic retention time). The effect of PSL-I on R1 was reversible within 10-12 days. At PSL-II, R1 required 2 days stop of feed for stability and resumed removal efficiency of phenol (15%) and COD (3%). R2 remained robust to sustain both PSLs and recovered within 15 days from peak influent concentrations of 1727 mg phenol/L (removal: 67%) and 324 mg SCN--/L (removal: 68-70%). In B1, effluent COD increased by 2%, though effluent phenol decreased by 3% than the pre-shock condition after PSL-I exposure. B2 acted similar to R2 when exposed to PSLs. The effect of PSL-I on R3 and B3 was negligible. However, at PSL-II R3 became vulnerable for nitrification, whereas phenol, COD and SCN- removal remained unaffected. In B3, PSL-II caused a decrease in phenol, SCN- and NH+4-N removal. In B3, stop of feed for 4 days also did not improve nitrification. The performance of the CMBR system was better than that of the FMBR system for organic shock load exposure in the presence of multiple pollutants.

Nitric Oxide Accumulation: The Evolutionary Trigger for Phytopathogenesis

Many publications highlight the importance of nitric oxide (NO) in plant–bacteria interactions, either in the promotion of health and plant growth or in pathogenesis. However, the role of NO in the signaling between bacteria and plants and in the fate of their interaction, as well as the reconstruction of their interactive evolution, remains largely unknown. Despite the complexity of the evolution of life on Earth, we explore the hypothesis that denitrification and aerobic respiration were responsible for local NO accumulation, which triggered primordial antagonistic biotic interactions, namely the first phytopathogenic interactions. N-oxides, including NO, could globally accumulate via lightning synthesis in the early anoxic ocean and constitute pools for the evolution of denitrification, considered an early step of the biological nitrogen cycle. Interestingly, a common evolution may be proposed for components of denitrification and aerobic respiration pathways, namely for NO and oxygen reductases, a theory compatible with the presence of low amounts of oxygen before the great oxygenation event (GOE), which was generated by Cyanobacteria. During GOE, the increase in oxygen caused the decrease of Earth’s temperature and the consequent increase of oxygen dissolution and availability, making aerobic respiration an increasingly dominant trait of the expanding mesophilic lifestyle. Horizontal gene transfer was certainly important in the joint expansion of mesophily and aerobic respiration. First denitrification steps lead to NO formation through nitrite reductase activity, and NO may further accumulate when oxygen binds NO reductase, resulting in denitrification blockage. The consequent transient NO surplus in an oxic niche could have been a key factor for a successful outcome of an early denitrifying prokaryote able to scavenge oxygen by NO/oxygen reductase or by an independent heterotrophic aerobic respiration pathway. In fact, NO surplus could result in toxicity causing “the first disease” in oxygen-producing Cyanobacteria. We inspected in bacteria the presence of sequences similar to the NO-producing nitrite reductase nirS gene of Thermus thermophilus, an extreme thermophilic aerobe of the Thermus/Deinococcus group, which constitutes an ancient lineage related to Cyanobacteria. In silico analysis revealed the relationship between the presence of nirS genes and phytopathogenicity in Gram-negative bacteria.

Performance of Agricultural Residue Media in Laboratory Denitrifying Bioreactors at Low Temperatures

Denitrifying bioreactors can be effective for removing nitrate from agricultural tile drainage; however, questions about cold springtime performance persist. The objective of this study was to improve the nitrate removal rate (NRR) of denitrifying bioreactors at warm and cold temperatures using agriculturally derived media rather than wood chips (WC). Corn ( L.) cobs (CC), corn stover (CS), barley ( L.) straw (BS), WC, and CC followed by a compartment of WC (CC+WC) were tested in laboratory columns for 5 mo at a 12-h hydraulic residence time in separate experiments at 15.5 and 1.5°C. Nitrate-N removal rates ranged from 35 to 1.4 at 15.5°C and from 7.4 to 1.6 g N m d at 1.5°C, respectively; NRRs were ranked CC > CC+WC > BS = CS > WC and CC ≥ CC+WC = CS ≥ BS > WC for 15.5 and 1.5°C, respectively. Although NRRs for CC were increased relative to WC, CC released greater amounts of carbon. Greater abundance of nitrous oxide (NO) reductase gene () was supported by crop residues than WC at 15.5°C, and CS and BS supported greater abundance than WC at 1.5°C. Production of NO relative to nitrate removal (NO) was consistently greater at 1.5°C (7.5% of nitrate removed) than at 15.5°C (1.9%). The NO was lowest in CC (1.1%) and CC-WC (0.9%) and greatest in WC (9.7%). Using a compartment of agricultural residue media in series before wood chips has the potential to improve denitrifying bioreactor nitrate removal rates, but field-scale verification is needed.

Impacts of Long-Term Irrigation of Domestic Treated Wastewater on Soil Biogeochemistry and Bacterial Community Structure

Freshwater scarcity and regulations on wastewater disposal have necessitated the reuse of treated wastewater (TWW) for soil irrigation, which has several environmental and economic benefits. However, TWW irrigation can cause nutrient loading to the receiving environments. We assessed bacterial community structure and associated biogeochemical changes in soil plots irrigated with nitrate-rich TWW (referred to as pivots) for periods ranging from 13 to 30 years. Soil cores (0 to 40 cm) were collected in summer and winter from five irrigated pivots and three adjacently located nonirrigated plots. Total bacterial and denitrifier gene abundances were estimated by quantitative PCR (qPCR), and community structure was assessed by 454 massively parallel tag sequencing (MPTS) of small-subunit (SSU) rRNA genes along with terminal restriction fragment length polymorphism (T-RFLP) analysis of nirK, nirS, and nosZ functional genes responsible for denitrification of the TWW-associated nitrate. Soil physicochemical analyses showed that, regardless of the seasons, pH and moisture contents (MC) were higher in the irrigated (IR) pivots than in the nonirrigated (NIR) plots; organic matter (OM) and microbial biomass carbon (MBC) were higher as a function of season but not of irrigation treatment. MPTS analysis showed that TWW loading resulted in the following: (i) an increase in the relative abundance of Proteobacteria, especially Betaproteobacteria and Gammaproteobacteria; (ii) a decrease in the relative abundance of Actinobacteria; (iii) shifts in the communities of acidobacterial groups, along with a shift in the nirK and nirS denitrifier guilds as shown by T-RFLP analysis. Additionally, bacterial biomass estimated by genus/group-specific real-time qPCR analyses revealed that higher numbers of total bacteria, Acidobacteria, Actinobacteria, Alphaproteobacteria, and the nirS denitrifier guilds were present in the IR pivots than in the NIR plots. Identification of the nirK-containing microbiota as a proxy for the denitrifier community indicated that bacteria belonged to alphaproteobacteria from the Rhizobiaceae family within the agroecosystem studied. Multivariate statistical analyses further confirmed some of the above soil physicochemical and bacterial community structure changes as a function of long-term TWW application within this agroecosystem.

Draft genome sequence of Bacillus azotoformans MEV2011, a (Co-) denitrifying strain unable to grow with oxygen

Bacillus azotoformans MEV2011, isolated from soil, is a microaerotolerant obligate denitrifier, which can also produce N₂ by co-denitrification. Oxygen is consumed but not growth-supportive. The draft genome has a size of 4.7 Mb and contains key genes for both denitrification and dissimilatory nitrate reduction to ammonium.

Draft genome sequence of Bacillus azotoformans MEV2011, a (Co-) denitrifying strain unable to grow with oxygen

Bacillus azotoformans MEV2011, isolated from soil, is a microaerotolerant obligate denitrifier, which can also produce N₂ by co-denitrification. Oxygen is consumed but not growth-supportive. The draft genome has a size of 4.7 Mb and contains key genes for both denitrification and dissimilatory nitrate reduction to ammonium.

Microbial ecology of denitrification in biological wastewater treatment

Globally, denitrification is commonly employed in biological nitrogen removal processes to enhance water quality. However, substantial knowledge gaps remain concerning the overall community structure, population dynamics and metabolism of different organic carbon sources. This systematic review provides a summary of current findings pertaining to the microbial ecology of denitrification in biological wastewater treatment processes. DNA fingerprinting-based analysis has revealed a high level of microbial diversity in denitrification reactors and highlighted the impacts of carbon sources in determining overall denitrifying community composition. Stable isotope probing, fluorescence in situ hybridization, microarrays and meta-omics further link community structure with function by identifying the functional populations and their gene regulatory patterns at the transcriptional and translational levels. This review stresses the need to integrate microbial ecology information into conventional denitrification design and operation at full-scale. Some emerging questions, from physiological mechanisms to practical solutions, for example, eliminating nitrous oxide emissions and supplementing more sustainable carbon sources than methanol, are also discussed. A combination of high-throughput approaches is next in line for thorough assessment of wastewater denitrifying community structure and function. Though denitrification is used as an example here, this synergy between microbial ecology and process engineering is applicable to other biological wastewater treatment processes.

Primers for overlooked nirK, qnorB, and nosZ genes of thermophilic Gram-positive denitrifiers

Although efforts have been made the past few years, knowledge on genomic and phenotypic diversity and occurrence of the denitrification ability in Gram-positive bacteria are still fragmentary. Many environmental monitoring approaches have used nir, nor, and nos genes as marker genes for detection of denitrification or denitrifying bacteria. However, primers used in these methods often fail to detect the genes in specific bacterial taxa, such as Gram-positive denitrifiers. In this study, novel primer sets specifically targeting nirK, qnorB, and nosZ genes of the Firmicute genus Geobacillus were developed by genomic mining and tested in parallel with commonly used primers on a set of phylogenetically closely related denitrifying geobacilli. Novel nirK and qnorB sequences were recovered from all strains tested, whereas nosZ was detected in part of the strain set, which was in agreement with observed phenotypes. Interspecies and modest intraspecies variations in amplified fragment length polymorphism (AFLP) patterns were observed, verifying presence of genomic variation within the strain set. Our study shows that closely related Gram-positive denitrifiers may differ in denitrification phenotype and genotype. But foremost, novel primers targeting very divergent nirK, qnorB, and nosZ gene sequences of Gram-positive denitrifiers, are now available for cultivation-independent environmental surveys.

Transferable denitrification capability of Thermus thermophilus

Laboratory-adapted strains of Thermus spp. have been shown to require oxygen for growth, including the model strains T. thermophilus HB27 and HB8. In contrast, many isolates of this species that have not been intensively grown under laboratory conditions keep the capability to grow anaerobically with one or more electron acceptors. The use of nitrogen oxides, especially nitrate, as electron acceptors is one of the most widespread capabilities among these facultative strains. In this process, nitrate is reduced to nitrite by a reductase (Nar) that also functions as electron transporter toward nitrite and nitric oxide reductases when nitrate is scarce, effectively replacing respiratory complex III. In many T. thermophilus denitrificant strains, most electrons for Nar are provided by a new class of NADH dehydrogenase (Nrc). The ability to reduce nitrite to NO and subsequently to N2O by the corresponding Nir and Nor reductases is also strain specific. The genes encoding the capabilities for nitrate (nar) and nitrite (nir and nor) respiration are easily transferred between T. thermophilus strains by natural competence or by a conjugation-like process and may be easily lost upon continuous growth under aerobic conditions. The reason for this instability is apparently related to the fact that these metabolic capabilities are encoded in gene cluster islands, which are delimited by insertion sequences and integrated within highly variable regions of easily transferable extrachromosomal elements. Together with the chromosomal genes, these plasmid-associated genetic islands constitute the extended pangenome of T. thermophilus that provides this species with an enhanced capability to adapt to changing environments.

Culturable bacterial flora associated with the dinoflagellate green Noctiluca miliaris during active and declining bloom phases in the Northern Arabian Sea

A massive algal bloom of the dinoflagellate Noctiluca miliaris (green) was located in the Northern Arabian Sea by IRS-P4-2 (OCM-II) for microbiological studies, during two consecutive cruises of February-March 2009. Culturable bacterial load during bloom were ≈ 2-3-fold higher in comparison to non-bloom waters and ranged from 3.20 × 10(5) to 6.84 × 10(5) cfu ml(-1). An analysis of the dominant heterotrophs associated with Noctiluca bloom resulted in phylogenetic and a detailed metabolic characterization of 70 bacterial isolates from an overlapping active and declining bloom phase location near north-central Arabian Sea. The active phase flora was dominated by Gram-positive forms (70.59 %), a majority of which belonged to Bacillus (35.29 %) of Firmicutes. As the bloom declined, Gram-negative forms (61.11 %) emerged dominant, and these belonged to a diverse γ-proteobacterial population consisting of Shewanella (16.67 %) and equal fractions of a Cobetia-Pseudomonas-Psychrobacter-Halomonas population (36.11 %). A Unifrac-based principal coordinate analysis of partial 16S rDNA sequences showed significant differences among the active and declining phase flora and also with reported endocytic flora of Noctiluca (red). A nonparametric multidimensional scaling (NMDS) of antibiogram helped differentiation among closely related strains. The organic matter synthesized by N. miliaris appears to be quickly utilized and remineralized as seen from the high efficiency of isolates to metabolize various complex and simple C/N substrates such as carbohydrates, proteins/amino acids, lipids, sulfide production from organic matter, and solubilize phosphates. The ability of a large fraction of these strains (50-41.67 %) to further aerobically denitrify indicates their potential for nitrogen removal from these high-organic microniches of the Noctiluca bloom in the Arabian Sea, also known for high denitrification activity. The results indicate that culturable euphotic bacterial associates of Noctiluca are likely to play a critical role in the biogeochemical ramifications of these unique seasonally emerging tropical open-water blooms of the Northern Arabian Sea.

Achromobacter animicus sp. nov., Achromobacter mucicolens sp. nov., Achromobacter pulmonis sp. nov. and Achromobacter spiritinus sp. nov., from human clinical samples

The phenotypic and genotypic characteristics of fourteen human clinical Achromobacter strains representing four genogroups which were delineated by sequence analysis of nusA, eno, rpoB, gltB, lepA, nuoL and nrdA loci, demonstrated that they represent four novel Achromobacter species. The present study also characterized and provided two additional reference strains for Achromobacter ruhlandii and Achromobacter marplatensis, species for which, thus far, only single strains are publicly available, and further validated the use of 2.1% concatenated nusA, eno, rpoB, gltB, lepA, nuoL and nrdA sequence divergence as a threshold value for species delineation in this genus. Finally, although most Achromobacter species can be distinguished by biochemical characteristics, the present study also highlighted considerable phenotypic intraspecies variability and demonstrated that the type strains may be phenotypically poor representatives of the species. We propose to classify the fourteen human clinical strains as Achromobacter mucicolens sp. nov. (with strain LMG 26685(T) [=CCUG 61961(T)] as the type strain), Achromobacter animicus sp. nov. (with strain LMG 26690(T) [=CCUG 61966(T)] as the type strain), Achromobacter spiritinus sp. nov. (with strain LMG 26692(T) [=CCUG 61968(T)] as the type strain), and Achromobacter pulmonis sp. nov. (with strain LMG 26696(T) [=CCUG 61972(T)] as the type strain).

Screening of anaerobic activities in sediments of an acidic environment: Tinto River

The Tinto River (Huelva, Spain) is a natural acidic rock drainage environment produced by the bio-oxidation of metallic sulfides from the Iberian Pyritic Belt. A geomicrobiological model of the different microbial cycles operating in the sediments was recently developed through molecular biological methods, suggesting the presence of iron reducers, methanogens, nitrate reducers and hydrogen producers. In this study, we used a combination of molecular biological methods and targeted enrichment incubations to validate this model and prove the existence of those potential anaerobic activities in the acidic sediments of Tinto River. Methanogenic, sulfate-reducing, denitrifying and hydrogen-producing enrichments were all positive at pH between 5 and 7. Methanogenic enrichments revealed the presence of methanogenic archaea belonging to the genera Methanosarcina and Methanobrevibacter. Enrichments for sulfate-reducing microorganisms were dominated by Desulfotomaculum spp. Denitrifying enrichments showed a broad diversity of bacteria belonging to the genera Paenibacillus, Bacillus, Sedimentibacter, Lysinibacillus, Delftia, Alcaligenes, Clostridium and Desulfitobacterium. Hydrogen-producing enrichments were dominated by Clostridium spp. These enrichments confirm the presence of anaerobic activities in the acidic sediments of the Tinto River that are normally assumed to take place exclusively at neutral pH.

Microbial CH(4) and N(2)O Consumption in Acidic Wetlands

Acidic wetlands are global sources of the atmospheric greenhouse gases methane (CH(4)), and nitrous oxide (N(2)O). Consumption of both atmospheric gases has been observed in various acidic wetlands, but information on the microbial mechanisms underlying these phenomena is scarce. A substantial amount of CH(4) is consumed in sub soil by aerobic methanotrophs at anoxic-oxic interfaces (e.g., tissues of Sphagnum mosses, rhizosphere of vascular plant roots). Methylocystis-related species are likely candidates that are involved in the consumption of atmospheric CH(4) in acidic wetlands. Oxygen availability regulates the activity of methanotrophs of acidic wetlands. Other parameters impacting on the methanotroph-mediated CH(4) consumption have not been systematically evaluated. N(2)O is produced and consumed by microbial denitrification, thus rendering acidic wetlands as temporary sources or sinks for N(2)O. Denitrifier communities in such ecosystems are diverse, and largely uncultured and/or new, and environmental factors that control their consumption activity are unresolved. Analyses of the composition of N(2)O reductase genes in acidic wetlands suggest that acid-tolerant Proteobacteria have the potential to mediate N(2)O consumption in such soils. Thus, the fragmented current state of knowledge raises open questions concerning methanotrophs and denitrifiers that consume atmospheric CH(4) and N(2)O in acidic wetlands.