Ecological control analysis: being(s) in control of mass flux and metabolite concentrations in anaerobic degradation processes

Emission behavior and impact assessment of gaseous volatile compounds in two typical rural domestic waste landfills

Landfill sites are sources of gaseous volatile compounds. The dumping area (LDA) and leachate storage pool (LSP) of two typical rural domestic waste landfill sites in north China (NLF) and southwest China (SLF) were investigated. We found that 45, 46, 61 and 68 volatile organic compounds (VOC) were present in the air of NLF-LDA, NLF-LSP, SLF-LDA, and SLF-LSP, respectively. And there were 27, 29, 35 and 37 kinds of odorous compounds being detected. Oxygenated compounds (>48.88%), chlorinated compounds (>6.85%), and aromatics (>5.46%), such as organic acid, 1-chlorobutane, and benzene, were the most abundant compounds in both landfills. The SLF-LDA had the highest olfactory effect, with a corresponding total odor activity value of 29,635.39. The ozone-formation potential analysis showed that VOCs emitted from SLF landfills had significantly higher potential for ozone formation than those from NLF landfills, with ozone generation potentials of 166.02, 225.86, 2511.82, and 1615.99 mg/m³ for the NLF-LDA, NLF-LSP, SLF-LDA, and SLF-LSP, respectively. Higher chronic toxicity and cancer risk of VOCs were found in the SLF according to method of Risk Assessment Information System. Based on the sensitivity analysis by the Monte Carlo method, concentrations of benzene, propylene oxide, propylene, trichloroethylene, and N-nitrosodiethylamine, along with exposure duration, daily exposure time, and annual exposure frequency, significantly impacted the risk levels. We provide a scientific basis, which reflects the need for controlling and reducing gaseous pollutants from landfills, particularly rural residential landfills, which may improve rural sanitation.

Niche partitioning of bacterial communities along the stratified water column in the Black Sea

The Black Sea is the largest semi‐closed permanently anoxic basin on our planet with long‐term stratification. The study aimed at describing the Black Sea microbial community taxonomic and functional composition within the range of depths spanning across oxic/anoxic interface, and to uncover the factors behind both their vertical and regional differentiation. 16S rRNA gene MiSeq sequencing was applied to get the data on microbial community taxonomy, and the PICRUSt pipeline was used to infer their functional profile. The normoxic zone was mainly inhabited by primary producers and heterotrophic prokaryotes (e.g., Flavobacteriaceae, Rhodobacteraceae, Synechococcaceae) whereas the euxinic zone—by heterotrophic and chemoautotrophic taxa (e.g., MSBL2, Piscirickettsiaceae, and Desulfarculaceae). Assimilatory sulfate reduction and oxygenic photosynthesis were prevailing within the normoxic zone, while the role of nitrification, dissimilatory sulfate reduction, and anoxygenic photosynthesis increased in the oxygen‐depleted water column part. Regional differentiation of microbial communities between the Ukrainian shelf and offshore zone was detected as well, yet it was significantly less pronounced than the vertical one. It is suggested that regional differentiation within a well‐oxygenated zone is driven by the difference in phytoplankton communities providing various substrates for the prokaryotes, whereas redox stratification is the main driving force behind microbial community vertical structure.

Bacteriome depiction and the trophic status of the largest Northern highland lake from Andes system: Lago de Tota, Boyacá, Colombia

Lago de Tota is the largest highland lake in Colombia and one of the most remarkable of Northern Andean Mountain range. This lake is under an anthropogenic-based eutrophication process as a consequence of non-sustainable agriculture practices developing nearby. Notable relationship between the trophic status and Bacteriome loop dynamics has been increasingly disclosed in lakes worldwide. We performed a 16S sequencing analysis to depict the bacterial community present and we inferred its potential gene function in Lago de Tota. Parameters for determining current trophic condition such as total nitrogen (TN), dissolved carbon (DOC), particulate organic matter (POM), and chlorophyll-a (chl-a) were measured. A total of 440 Operational Taxonomic Units (OTUs) arranged into 50 classes were identified based on V3-V4 regions of the 16S rRNA gene, harboring high-frequent likely found environmental classes such as Actinobacteria, Gammaproteobacteria, Bacteroidia, Acidimicrobia, and Verrucomicrobiae. A total of 26 bacterial classes configure most abundant predicted functional processes involved in organic matter decomposition (i.e., carbohydrate metabolism, amino acid metabolism, xenobiotic biodegradation, and energy metabolism). In general, Actinobacteria, Alphaproteobacteria, and Gammaproteobacteria show the highest potential gene functional contributors, although other low-frequent classes OTUs are also relevant in processes of carbohydrate metabolism, xenobiotic biodegradation, and energy metabolism. The Trophic State Index indicates an oligo-mesotrophic status, and additional variables measured (i.e., POM, DOC) suggest the increasing carbon accumulation. Results provide preliminary evidence for several bacteria groups related to eutrophication of Lago de Tota. Under this picture, we suggest that further studies for Bacteriome loop spatial-temporal description are essential to inform local water quality monitoring strategies.

Composition and profiles of volatile organic compounds during waste decomposition by the anaerobic bacteria purified from landfill

Volatile organic compounds (VOCs) become concerned pollutants in landfill gases, and their composition and concentration varied significantly during waste decomposition. Many environmental factors are known to affect VOC emissions, while the effect of indigenous bacteria in wastes on VOC production remains elusive. In this study, a simplified anaerobic degradation experiment, with the single substrate and the purified bacteria from a landfill, was set up to measure the degradation process and the dynamic changes of VOCs. The experiment excluded the abiotic factors for VOC variation. The two isolated bacteria, identified as Sporanaerobacter acetigenes and Clostridium sporogenes, could anaerobically ferment amino acids by Stickland reaction. They produced 51 and 57 species of VOCs in the experiment, respectively. The concentration changes of VOCs over bacterial growth and fermentation were clustered into four types by principal component analysis: three profiles were regular, similar to the variation of nitrate, hydrogen sulfide, and the major fermentation products (carbon dioxide, ammonium, and volatile organic acids), respectively; while one profile was unique to any degradation indicator. The various concentration profiles indicated different origins for VOCs, possibly from the extracellular environment, fermentation, and secondary reactions. The findings provide insights into the understanding of VOC diversity and variability during waste decomposition.

Formation of anaerobic granules and microbial community structure analysis in anaerobic hydrolysis denitrification reactor

An anaerobic hydrolysis denitrification (AnHD) process was developed to pretreat municipal wastewater for integrating partial nitration/anammox process. The results indicated that the carbon to nitrogen (C/N) ratio of municipal wastewater changed from 4.4 ± 0.3 to 2.2 ± 0.2 after pretreatment by AnHD process, which was favorable to the partial nitration/anammox process. The influent C/N ratio had influence on the formation of anaerobic granules. Two intrinsic factors, cyclic diguanylic acid (c-di-GMP) concentration and core bacterial community, were mainly responsible for the anaerobic granular formation. The higher c-di-GMP content increased the extracellular polymeric substances and decreased the motility of the bacteria, which was beneficial for the formation of anaerobic granules. The microbial community analysis showed that the lactic acid bacteria (Lactococcus) was the core bacteria during anaerobic hydrolysis process, while the denitrifying bacteria (Denitratisoma and unclassified Comamonadaceae) were the core bacterial community during AnHD process, which were responsible for nitrogen removal and anaerobic granular formation.

Achieving mainstream nitrogen removal through simultaneous partial nitrification, anammox and denitrification process in an integrated fixed film activated sludge reactor

The anaerobic ammonium oxidation (anammox) is becoming a critical technology for energy neutral in mainstream wastewater treatment. However, the presence of chemical oxygen demanding in influent would result in a poor nitrogen removal efficiency during the deammonification process. In this study, the simultaneous partial nitrification, anammox and denitrification process (SNAD) for mainstream nitrogen removal was investigated in an integrated fixed film activated sludge (IFAS) reactor. SNAD-IFAS process achieved a total nitrogen (TN) removal efficiency of 72 ± 2% and an average COD removal efficiency was 88%. The optimum COD/N ratio for mainstream wastewater treatment was 1.2 ± 0.2. Illumina sequencing analysis and activity tests showed that anammox and denitrifying bacteria were the dominant nitrogen removal microorganism in the biofilm and the high COD/N ratios (≥2.0) leaded to the proliferation of heterotrophic bacteria (Hydrogenophaga) and nitrite-oxidizing bacteria (Nitrospira) in the suspended sludge. Network analysis confirmed that anammox bacteria (Candidatus Kuenenia) could survive in organic matter environment due to that anammox bacteria displayed significant co-occurrence through positive correlations with some heterotrophic bacteria (Limnobacter) which could protect anammox bacteria from hostile environments. Overall, the results of this study provided more comprehensive information regarding the community composition and assemblies in SNAD-IFAS process for mainstream nitrogen removal.

Integrating Ecological and Engineering Concepts of Resilience in Microbial Communities

Many definitions of resilience have been proffered for natural and engineered ecosystems, but a conceptual consensus on resilience in microbial communities is still lacking. We argue that the disconnect largely results from the wide variance in microbial community complexity, which range from compositionally simple synthetic consortia to complex natural communities, and divergence between the typical practical outcomes emphasized by ecologists and engineers. Viewing microbial communities as elasto-plastic systems that undergo both recoverable and unrecoverable transitions, we argue that this gap between the engineering and ecological definitions of resilience stems from their respective emphases on elastic and plastic deformation, respectively. We propose that the two concepts may be fundamentally united around the resilience of function rather than state in microbial communities and the regularity in the relationship between environmental variation and a community's functional response. Furthermore, we posit that functional resilience is an intrinsic property of microbial communities and suggest that state changes in response to environmental variation may be a key mechanism driving functional resilience in microbial communities.

Epidemic control analysis: designing targeted intervention strategies against epidemics propagated on contact networks

In cases where there are limited resources for the eradication of an epidemic, or where we seek to minimise possible adverse impacts of interventions, it is essential to optimise the efficacy of control measures. We introduce a new approach, Epidemic Control Analysis (ECA), to design effective targeted intervention strategies to mitigate and control the propagation of infections across heterogeneous contact networks. We exemplify this methodology in the context of a newly developed individual-level deterministic Susceptible-Infectious-Susceptible (SIS) epidemiological model (we also briefly consider applications to Susceptible-Infectious-Removed (SIR) dynamics). This provides a flexible way to systematically determine the impact of interventions on endemic infections in the population. Individuals are ranked based on their influence on the level of infectivity. The highest-ranked individuals are prioritised for targeted intervention. Many previous intervention strategies have determined prioritisation based mainly on the position of individuals in the network, described by various local and global network centrality measures, and their chance of being infectious. Comparisons of the predictions of the proposed strategy with those of widely used targeted intervention programmes on various model and real-world networks reveal its efficiency and accuracy. It is demonstrated that targeting central individuals or individuals that have high infection probability is not always the best strategy. The importance of individuals is not determined by network structure alone, but can be highly dependent on the infection dynamics. This interplay between network structure and infection dynamics is effectively captured by ECA.

Toward quantitative understanding on microbial community structure and functioning: a modeling-centered approach using degradation of marine oil spills as example

Molecular ecology approaches are rapidly advancing our insights into the microorganisms involved in the degradation of marine oil spills and their metabolic potentials. Yet, many questions remain open: how do oil-degrading microbial communities assemble in terms of functional diversity, species abundances and organization and what are the drivers? How do the functional properties of microorganisms scale to processes at the ecosystem level? How does mass flow among species, and which factors and species control and regulate fluxes, stability and other ecosystem functions? Can generic rules on oil-degradation be derived, and what drivers underlie these rules? How can we engineer oil-degrading microbial communities such that toxic polycyclic aromatic hydrocarbons are degraded faster? These types of questions apply to the field of microbial ecology in general. We outline how recent advances in single-species systems biology might be extended to help answer these questions. We argue that bottom-up mechanistic modeling allows deciphering the respective roles and interactions among microorganisms. In particular constraint-based, metagenome-derived community-scale flux balance analysis appears suited for this goal as it allows calculating degradation-related fluxes based on physiological constraints and growth strategies, without needing detailed kinetic information. We subsequently discuss what is required to make these approaches successful, and identify a need to better understand microbial physiology in order to advance microbial ecology. We advocate the development of databases containing microbial physiological data. Answering the posed questions is far from trivial. Oil-degrading communities are, however, an attractive setting to start testing systems biology-derived models and hypotheses as they are relatively simple in diversity and key activities, with several key players being isolated and a high availability of experimental data and approaches.

Systems approaches to microbial communities and their functioning

Recent advances in molecular microbial ecology and systems biology enhance insight into microbial community structure and functioning. They provide conceptual and technical bases for the translation of species-data and community-data into a model framework accounting for the functioning of and interactions between metabolic networks of species in multispecies environments. Function-directed and single cell-directed approaches supplement and improve metagenomics-derived community information. The topology of the metabolic network, reconstructed from a species' genome sequence, provides insight into its metabolic environments and interactions with other microorganisms. Progress in the theoretical and experimental analysis of flux through metabolic networks paves the way for their application at the community level, contributing to understanding of material flows between and within species and their resilience toward perturbations.

Integration of molecular functions at the ecosystemic level: breakthroughs and future goals of environmental genomics and post-genomics

Environmental genomics and genome-wide expression approaches deal with large-scale sequence-based information obtained from environmental samples, at organismal, population or community levels. To date, environmental genomics, transcriptomics and proteomics are arguably the most powerful approaches to discover completely novel ecological functions and to link organismal capabilities, organism-environment interactions, functional diversity, ecosystem processes, evolution and Earth history. Thus, environmental genomics is not merely a toolbox of new technologies but also a source of novel ecological concepts and hypotheses. By removing previous dichotomies between ecophysiology, population ecology, community ecology and ecosystem functioning, environmental genomics enables the integration of sequence-based information into higher ecological and evolutionary levels. However, environmental genomics, along with transcriptomics and proteomics, must involve pluridisciplinary research, such as new developments in bioinformatics, in order to integrate high-throughput molecular biology techniques into ecology. In this review, the validity of environmental genomics and post-genomics for studying ecosystem functioning is discussed in terms of major advances and expectations, as well as in terms of potential hurdles and limitations. Novel avenues for improving the use of these approaches to test theory-driven ecological hypotheses are also explored.

The little bacteria that can - diversity, genomics and ecophysiology of 'Dehalococcoides' spp. in contaminated environments

The fate and persistence of chlorinated organics in the environment have been a concern for the past 50 years. Industrialization and extensive agricultural activities have led to the accumulation of these pollutants in the environment, while their adverse impact on various ecosystems and human health also became evident. This review provides an update on the current knowledge of specialized anaerobic bacteria, namely ‘Dehalococcoides’ spp., which are dedicated to the transformation of various chlorinated organic compounds via reductive dechlorination. Advances in microbiology and molecular techniques shed light into the diversity and functioning of Dehalococcoides spp. in several different locations. Recent genome sequencing projects revealed a large number of genes that are potentially involved in reductive dechlorination. Molecular approaches towards analysis of diversity and expression especially of reductive dehalogenase‐encoding genes are providing a growing body of knowledge on biodegradative pathways active in defined pure and mixed cultures as well as directly in the environment. Moreover, several successful field cases of bioremediation strengthen the notion of dedicated degraders such as Dehalococcoides spp. as key players in the restoration of contaminated environments.

What is microbial community ecology?

The activities of complex communities of microbes affect biogeochemical transformations in natural, managed and engineered ecosystems. Meaningfully defining what constitutes a community of interacting microbial populations is not trivial, but is important for rigorous progress in the field. Important elements of research in microbial community ecology include the analysis of functional pathways for nutrient resource and energy flows, mechanistic understanding of interactions between microbial populations and their environment, and the emergent properties of the complex community. Some emergent properties mirror those analyzed by community ecologists who study plants and animals: biological diversity, functional redundancy and system stability. However, because microbes possess mechanisms for the horizontal transfer of genetic information, the metagenome may also be considered as a community property.

Obligate oil-degrading marine bacteria

Over the past few years, a new and ecophysiologically unusual group of marine hydrocarbon-degrading bacteria - the obligate hydrocarbonoclastic bacteria (OHCB) - has been recognized and shown to play a significant role in the biological removal of petroleum hydrocarbons from polluted marine waters. The introduction of oil or oil constituents into seawater leads to successive blooms of a relatively limited number of indigenous marine bacterial genera--Alcanivorax, Marinobacter, Thallassolituus, Cycloclasticus, Oleispira and a few others (the OHCB)--which are present at low or undetectable levels before the polluting event. The types of OHCB that bloom depend on the latitude/temperature, salinity, redox and other prevailing physical-chemical factors. These blooms result in the rapid degradation of many oil constituents, a process that can be accelerated further by supplementation with limiting nutrients. Genome sequencing and functional genomic analysis of Alcanivorax borkumensis, the paradigm of OHCB, has provided significant insights into the genomic basis of the efficiency and versatility of its hydrocarbon utilization, the metabolic routes underlying its special hydrocarbon diet, and its ecological success. These and other studies have revealed the potential of OHCB for multiple biotechnological applications that include not only oil pollution mitigation, but also biopolymer production and biocatalysis.