Anaerobic Estuarine Sediment Research Articles

Anaerobic degradation of organic carbon supports uncultured microbial populations in estuarine sediments

BackgroundA large proportion of prokaryotic microbes in marine sediments remains uncultured, hindering our understanding of their ecological functions and metabolic features. Recent environmental metagenomic studies suggested that many of these uncultured microbes contribute to the degradation of organic matter, accompanied by acetogenesis, but the supporting experimental evidence is limited.ResultsEstuarine sediments were incubated with different types of organic matters under anaerobic conditions, and the increase of uncultured bacterial populations was monitored. We found that (1) lignin stimulated the increase of uncultured bacteria within the class Dehalococcoidia. Their ability to metabolize lignin was further supported by the presence of genes associated with a nearly complete degradation pathway of phenolic monomers in the Dehalococcoidia metagenome-assembled genomes (MAGs). (2) The addition of cellulose stimulated the increase of bacteria in the phylum Ca. Fermentibacterota and family Fibrobacterales, a high copy number of genes encoding extracellular endoglucanase or/and 1,4-beta-cellobiosidase for cellulose decomposition and multiple sugar transporters were present in their MAGs. (3) Uncultured lineages in the order Bacteroidales and the family Leptospiraceae were enriched by the addition of casein and oleic acid, respectively, a high copy number of genes encoding extracellular peptidases, and the complete β-oxidation pathway were found in those MAGs of Bacteroidales and Leptospiraceae, respectively. (4) The growth of unclassified bacteria of the order Clostridiales was found after the addition of both casein and cellulose. Their MAGs contained multiple copies of genes for extracellular peptidases and endoglucanase. Additionally, 13C-labeled acetate was produced in the incubations when 13C-labeled dissolved inorganic carbon was provided.ConclusionsOur results provide new insights into the roles of microorganisms during organic carbon degradation in anaerobic estuarine sediments and suggest that these macro and single molecular organic carbons support the persistence and increase of uncultivated bacteria. Acetogenesis is an additional important microbial process alongside organic carbon degradation.8vg1mZsw3sS2b3Wiiq9h8HVideo

Plant‐based foods and the gut microbiome: A research profile of Franck Carbonero

Plant‐based foods and the gut microbiome: A research profile of Franck Carbonero

A metagenomic assessment of microbial communities in anaerobic bioreactors and sediments: Taxonomic and functional relationships

The present study used metagenomic sequencing, metagenome assembly and physical-chemical analysis to describe taxonomically and functionally 3 anaerobic bioreactors treating manure (LI), brewery (BR) and cornmeal (CO) wastes, and an anaerobic estuarine sediment (ES). Proteobacteria, Firmicutes, Euryarchaeota and Bacteroidetes were the most abundant Phyla in all metagenomes. A bacteria/archaea ratio of 3.4 was found in the industrial full-scale anaerobic bioreactors BR and CO, while ratios greater than 10 were found for LI and ES. Canonical correspondence analysis showed that environmental variables such as chemical oxygen demand, lipid content, and ammonium nitrogen influenced the ordination of taxonomic groups. Mesotoga prima was linked to high-temperature conditions, particularly in the BR bioreactor, along with the presence of heat shock proteins genes. Likewise, the hydrogenotrophic methanogen, Methanoregula formicica, was associated with high ammonium concentration in LI bioreactor. The interactions of microbes with specific methanogenic pathways were identified using Clusters of Orthologous Groups (COG) functions, while metagenome-assembled genomes (MAGs) further confirmed relationships between taxa and functions. Our results provide valuable information to understand microbial processes in anaerobic environments.

Impact of coplanar PCBs on microbial communities in anaerobic estuarine sediments

The toxicity of three coplanar PCBs on microbial communities of an estuarine sediment were assessed. Sediment slurries were amended with 2, 10 and 50 mg/L of 345-4 CB, 345-34 CB and 345-345 CB, respectively under anaerobic conditions. The fate and effects of these coplanar PCBs were studied over 250 days. Bacterial communities in sediment slurries were described by dehrdogenase activity and by bacterial populations deduced from the clone libraries. Dechlorination of 345-4 CB and 345-34 CB occurred at least after 100 days of incubation, but dechlorination of 345-345 CB was not observed over the entire incubation period. However, time profiles of dehydrogenase activity were similar in sediment slurries amended with 345-4 CB, 345-34 CB or 345-345 CB. After normalization of the effect of acetone we found that dehydrogenase activity was increased in sediment slurries amended with 50 mg/L, but were inhibited in those amended with 2 and 10 mg/L of coplanar PCBs. Extra addition of electron donors plus sulfate or sulfate could increase dehydrogenase activity significantly. The major microbial populations in the sediment slurries incubated with 2, 10, and 50 mg/L of 345-4 CB were δ-Proteobacteria, Chloroflexi, and ϵ-Proteobacteria, respectively. This study shows that (1) dechlorination of coplanar PCBs did not change their effects on microbial metabolic activities, (2) concentration of coplanar PCBs had effects on microbial metabolic activities and community composition, (3) extra addition of electron donors plus sulfate or sulfate could increase dehydrogenase activity significantly, but this did not always lead to higher dechlorination rates, (4) coplanar PCBs induced perturbations of sediment microbial communities in terms of population structures (but not always as an inhibition).

Producing 13C NMR, Infrared Absorption, and Electron Ionization Mass Spectrometric Data Models of the Monodechlorination of Chlorobenzenes, Chlorophenols, and Chloroanilines

We have developed four spectroscopic data-activity relationship (SDAR) models of monodechlorination of 32 chlorinated benzene compounds in anaerobic estuarine sediment. The SDAR models were based on combinations of 13C nuclear magnetic resonance (NMR), infrared absorption (IR), and electron ionization mass spectrometric (EI MS) data. The SDAR models segregated the 32 compounds into 17 readily monodechlorinated compounds and 15 not readily monodechlorinated compounds. The SDAR model based on 13C NMR, IR, and EI MS data gave a leave-one-out cross-validation of 93.8%. The SDAR model based on a composite of 13C NMR and IR data gave a leave-one-out cross-validation of 90.6%. The SDAR model based on a composite of IR and EI MS data gave a leave-one-out cross-validation of 84.4%. The SDAR model based on a composite of 13C NMR and EI MS data gave a leave-one-out cross-validation of 84.4%. These reliable SDAR models provide a rapid and simple way to predict whether a chlorinated benzene compound will readily go through monodechlorination. The FDA has filed a patent application on methods of using any combination of spectral data (NMR, MS, UV-vis, IR, and fluorescence, phosphorescence) to model a chemical, physical, or biological endpoint.

Reductive transformations of halogenated aromatics in anaerobic estuarine sediment: kinetics, products and pathways

The transformation of different classes of halogenated aromatic compounds in sulfidogenic sediment slurries was examined in laboratory incubation experiments. The results indicated that several processes were shown to occur, leading to the formation of a number of intermediate metabolites. The kinetics of transformation followed a first-order reaction mechanism, with k values in the range of 1.67 and 0.0005 day −1 or half-lives of 0.4 and 1386 days. The order of transformation rates among different classes of compounds was: phenols > anilines > benzenes > pesticides. The pathway of transformation among single-ring aromatic compounds indicated that ortho and para halogen removal was the predominant compared to meta halogen removal.

Interactions of Cd and Cu in anaerobic estuarine sediments. II. Bioavailability, body burdens and respiration effects as related to geochemical partitioning

AbstractThe relationship between Cd and Cu distribution in sediment geochemical fractions and their bioavailability was studied. A fine‐sandy textured estuarine sediment was treated with all combinations of 0, 2.5, and 5 mg/kg Cd and 0, 12, and 25 mg/kg Cu using the chloride salts of each metal. Grass shrimp (Palaemonetes pugio), blue mussel (Mytilus edulis), and hard clam (Mercenaria mercenaria) were exposed to the treated sediments in aquaria with 20 ppt artificial seawater for 14 d. Sediments were sequentially extracted before and after organism exposure to determine the exchangeable, easily reducible, organic‐sulfide, moderately reducible, and acid extractable phases. Low mortalities were observed for all organism types and none were attributable to any of the treatments. The Cd and Cu concentrations in the easily reducible and organic‐sulfide phases were found to be significantly related to the bio‐availability of these metals. The most highly significant relationship was established between Cd in the easily reducible phase and body burden of Cd in the blue mussel. Notable interactions were found between Cd and Cu in some of the geochemical phases, body burdens, and respiration rates. Metal uptake, respiration, and interactions were highly dependent on the test species. A significant correlation was found between increased body burden and depressed respiration for Cd but not for Cu. Multiple regression models are used to describe these relationships. It appears that the interactive responses in the organisms are driven primarily by the sediment geochemical effects and mediated by individual organism processes. These results underscore the necessity of multicomponent (multielement) studies in assessing the fate and effects of toxic elements in the environment.

Interactions of Cd and Cu in anaerobic estuarine sediments. I. Partitioning in geochemical fractions of sediments

Partitioning of Cd and Cu between geochemical fractions of an anaerobic estuarine sediment was determined after equilibrating fine-sandy sediment with different combinations of added Cd (0, 2.5, 5 mg/kg) and Cu(0, 12.5, 25 mg/kg). Sediments were placed in aquaria with 20 ppt seawater where bioassay test organisms were exposed for 14 d. At the start and conclusion of the experimental period, sediments were sequentially extracted to determine the elemental content of the exchangeable (EP), easily reducible (ERP), organic- sulfide (OSP), moderately reducible (MRP), and acid extractable (AEP) phases. Partitioning of the metals in both the native and treated sediments was, for Cd: OSP {much_gt} ERP > AEP > EP (MRP was below detection) and for Cu: OSP {much_gt} AEP > ERP > MRP > EP. Cadmium extracted in all phases and Cu in the EP, RP, and OSP were proportional to the respective treatments. The EP-Cd, ERP-Cd, and OSP-Cd were affected by the Cu treatment and significant interactions occurred between Cd and Cu for the EP-Cd, ERP-Cd, OSP-Cd, EP-Cu, and ERP-Cu. Increasing levels of applied Cd and Cu resulted in greater amounts of EP-Cd and ERP-Cd, fractions that are the most bioavailable and the most readily available for desorption intomore » the water column. A significant conclusion is that the input of nontoxic metals may affect the geochemical phase distribution, potential bioavailability, and toxicity of native sediment metals.« less

Transformations of chloronitrobenzenes in anaerobic sediment

The transformations of chloronitrobenzenes (CNBs) in anaerobic estuarine sediment were examined. The sediment had been preexposed to various anthropogenic chemicals from the surrounding industries. The sulfate content of the interstitial and overlaying waters was approximately 20 mmole/1 indicating that the sediment was sulfidogenic. All the CNBs tested transformed without any lag period. The kinetic data followed a first-order reaction mechanism with rate constants ranging from 0.216 to 0.866 day −1 or half-lives from 0.8 to 3.2 days. The intermediates detected in the experiment indicated that the reduction of the nitro group was the first stage in the transformation of chloronitro aromatic compounds, resulting in the formation of corresponding chloroanilines (CAs). The CAs further transformed via ortho and para dechlorination pathways.

Dechlorination of chlorobenzenes in anaerobic estuarine sediment

The reductive dechlorination of chlorobenzenes (CBs) in an anaerobic estuarine sediment was examined. The sediment was preexposed to various anthropogenic chemicals from the surrounding industries. The sulfate content (20 mmoles/l) in the interstitial waters indicated that the sediment was sulfidogenic. All the CBs were transformed following a first-order reaction kinetics with rate constants ranging from 0.0016 to 0.0389 day−1 or half-lives between 17 and 433 days. Disappearance of CBs in autoclaved sediment were observed but to a much less extent than in the test sediment. Detected intermediates indicated that the removal of chlorine atom occurred at all possible positions on the aromatic ring. The contribution of different dechlorination pathways were estimated using branched chain first-order irreversible reaction kinetics. The results showed that the preferential dechlorination was in the following order: two chlorine atoms on both sides > one of the adjacent chlorine atoms > chlorine with no adjacent chlorine atoms. The major pathway observed for CBs followed a thermodynamically most favorable step that gave the highest energy for dechlorination.

Pathway and Rate of Chlorophenol Transformation in Anaerobic Estuarine Sediment

The dechlorination of chlorophenols (CPs) in anaerobic estuarine sediment was studied. The sediment used was fairly contaminated with various anthropogenic chemicals from the surrounding industries. The sulfate content of the interstitial and overlying waters was approximately 20 mmol/L, and the sediment was apparently sulfidogenic. All 13 CPs tested transformed following a first-order reaction kinetics. The rate constants for CP disappearance ranged between 0.010 and 0.38 day-1 or had half-lives between 1.8 and 70 days. The intermediates detected in the experiment indicated that the ortho-dechlorination was the preferred pathway. The disappearance of the parent compound and the accumulation and disappearance of dechlorinated intermediates were simulated using a branched chain first-order irreversible reaction kinetics, and the contributions of different pathways were estimated. A comparison of the estimated rate constants with the redox potential of the reaction showed that the hypothesis of microbial selection of most thermodynamically favorable pathways observed for chlorobenzene dechlorination was not applicable for CPs.

Dechlorination of chlorobenzenes in anaerobic estuarine sediment

The reductive dechlorination of chlorobenzenes (CBs) in an anaerobic estuarine sediment was examined. The sediment was preexposed to various anthropogenic chemicals from the surrounding industries. The sulfate content (20 mmoles/l) in the interstitial waters indicated that the sediment was sulfidogenic. All the CBs were transformed following a first-order reaction kinetics with rate constants ranging from 0.0016 to 0.0389 day-1 or half-lives between 17 and 433 days. Disappearance of CBs in autoclaved sediment were observed but to a much less extent than in the test sediment. Detected intermediates indicated that the removal of chlorine atom occurred at all possible positions on the aromatic ring. The contribution of different dechlorination pathways were estimated using branched chain first-order irreversible reaction kinetics. The results showed that the preferential dechlorination was in the following order: two chlorine atoms on both sides > one of the adjacent chlorine atoms > chlorine with no adjacent chlorine atoms. The major pathway observed for CBs followed a thermodynamically most favorable step that gave the highest energy for dechlorination.

Fenbutatin acute toxicity on Artemia nauplii: effects of sublethal concentrations on ATPase activity.

During the last decades, the use of organotin compounds has steadily increased. The numerous applications of these compounds are primarily in industry as stabilizers for PVC, in agriculture as miticides and fungicides and in the marine environment as antifoulants. The increasing annual usage of organotin compounds raises the possibility of environmental pollution. The toxicity and degradation of organotins in the environment depends strongly on the number and nature of substituents (Muller 1987). In water, triphenyltin compounds decompose slowly (Bock 1981). Persistence of at least 8 months was found when triphenyltin was used against water snails at concentration of 1.0 ppm ( Deschiens and Floch 1963). Organotin compounds in the aquatic environment accumulate in the microlayer of the water surface, are readily adsorbed in sediments and on suspended particulates (Chernega et al. 1971, Cooney and Wuertz 1989). The half-life of organotins was found to be up to 5 months in freshwater sediments (Maguire and Tkacz 1985) and up to 2 years in deep and anaerobic estuarine sediments (Waldock et al.1990). Among organotins trisubstituted compounds are generally the most toxic to fish, to microorganisms and to other aquatic inhabitants (Bock 1981, Cooney and Wuertz 1989). Whereas the adverse effects of tributyltin, the main representative of antifouling agents , on the homeostasis of the aquatic ecosystems has been studied, few data are available concerning the environmental impact of the trisubstituted organotins used in agriculture as miticides. The aim of this project is to determine the median lethal concentration of the organotins used as miticides, in nauplii of the marine crustacea Artemia and to study the effects of sublethal concentrations on the activity of ATPase enzymatic system. In this study we will present the results from the experimentation with fenbutatin on the survival and ATPase activity of Artemia nauplii.

Partitioning of Cd in geochemical fractions of anaerobic estuarine sediments

Distribution of Cd in geochemical fractions of anaerobic estuarine sediments was determined before and after treatment of the sediments with added Cd. Portions of three sediment types (sandy, silty, and clayey) were treated with 5 and 10 mg kg−1 Cd as CdCl2 and each type had an untreated control. Sediments were sampled at the start and at the conclusion of a 14 day laboratory bioaccumulation study. Each set was promptly extracted using a sequential technique for exchangeable, easily reducible, organic-sulphide, moderately reducible, and acid extractable phases. In the non-treated sediments, approximately 64% of the naturally occurring Cd was in the acid extractable phase with most of the balance in the organicsulphide phase (OSP). There was a similar amount of Cd in the acid extractable phase of all treatments of all sediments. For the treated sediments, the majority of the Cd was found in the OSP and ranged from 56% to 85% for all treatments and sediments. At the end of the experiment, a greater and more consistent level of Cd was present in the OSP (from 76% to 92%). These results show an initially rapid conversion of most of the added soluble Cd to the OSP with conversion of up to 92% of applied Cd to this phase within 14 days. The bulk of the OSP Cd is postulated to occur as sulphides which are an important reservoir of sediment Cd. Addition of Cd had no effect on the geochemical distribution of native Cu, Fe, Mn, Ni, Pb, or Zn.

The application of compound bi-directional flow diffusion chemostats to the study of microbial interactions

A multi-stage bi-directional chemostat system has been developed in which solutes but not cells are allowed to diffuse between the individual growth chambers which are separated by 0.2 micron pore size polyvinyledene difluoride membranes. The experimental system enables the generation of physico-chemical gradients which, together with the spatial separation of the individual microbial processes, provides a useful laboratory model to study microbial interactions. This paper describes the construction of a multi-stage diffusion chemostat and its application in studying carbon flow in anaerobic estuarine sediments. Populations of Clostridium butyricum, Desulfovibrio desulfuricans and Chromatium vinosum were grown in the compound diffusion chemostat at a dilution rate of 0.03 h−1 at 25°C, and the effects of inorganic nitrogen source and availability on carbon flow and individual cell populations were determined. C. butyricum and D. desulfuricans both used NO−3 as an e− acceptor with an increase in cell numbers. Under these growth conditions, free S2− concentrations were lower, resulting in more stable cell populations than in comparable cultures grown on NH+4 as nitrogen source.

The application of compound bi-directional flow diffusion chemostats to the study of microbial interactions

A multi-stage bi-directional chemostat system has been developed in which solutes but not cells are allowed to diffuse between the individual growth chambers which are separated by 0.2 micron pore size polyvinyledene difluoride membranes. The experimental system enables the generation of physico-chemical gradients which, together with the spatial separation of the individual microbial processes, provides a useful laboratory model to study microbial interactions. This paper describes the construction of a multi-stage diffusion chemostat and its application in studying carbon flow in anaerobic estuarine sediments. Populations of Clostridium butyricum, Desulfovibrio desulfuricans and Chromatium vinosum were grown in the compound diffusion chemostat at a dilution rate of 0.03 h −1 at 25°C, and the effects of inorganic nitrogen source and availability on carbon flow and individual cell populations were determined. C. butyricum and D. desulfuricans both used NO − 3 as an e − acceptor with an increase in cell numbers. Under these growth conditions, free S 2− concentrations were lower, resulting in more stable cell populations than in comparable cultures grown on NH + 4 as nitrogen source.

Sulfide control of cadmium and copper concentrations in anaerobic estuarine sediments

Equilibrium concentrations of the toxic trace metals copper and cadmium were calculated for the physico-chemical conditions characterizing pore waters of anaerobic estuarine sediments using available thermodynamic data and assuming simple sulfide minerals control solubilities. Polysulfide complexes are responsible for the solubility of copper in the cuprous (Cu(I)) oxidation state. Predicated copper concentrations, assuming covellite (CuS) is the controlling solid phase, are in reasonable agreement with copper analyses in a wide range of sulfidic waters and sediment pore waters. In the absence of thermodynamic data, no account could be taken of possible polysulfide complexes of cadmium. However, bisulfide complexes appear to account satisfactorily for observed solubilities assuming the existence of greenockite (CdS) as the controlling solid phase. Anaerobic estuarine sediments may act as a sink for copper and cadmium in the common situation in which free sulfide concentrations are controlled by the coexistence of iron sulfide and iron oxide minerals. However, where free sulfides reach high concentrations of 10 −3 M or more, the concomitant increase in concentration of bisulfide and polysulfide complexes may result in the sediments acting as a source of copper and cadmium.