Relationships between soil organic matter, nutrients, bacterial community structure, and the performance of microbial fuel cells

Microbial fuel cells (MFCs) offer the potential for generating electricity, mitigating greenhouse gas emissions, and bioremediating pollutants through utilization of a plentiful renewable resource: soil organic carbon. We analyzed bacterial community structure, MFC performance, and soil characteristics in different microhabitats within MFCs constructed from agricultural or forest soils in order to determine how soil type and bacterial dynamics influence MFC performance. Our results indicated that MFCs constructed from agricultural soil had power output about 17 times that of forest soil-based MFCs and respiration rates about 10 times higher than forest soil MFCs. Agricultural soil MFCs had lower C:N ratios, polyphenol content, and acetate concentrations than forest soil MFCs. Bacterial community profile data indicate that the bacterial communities at the anode of the high power MFCs were less diverse than in low power MFCs and were dominated by Deltaproteobacteria, Geobacter, and to a lesser extent, Clostridia, while low-power MFC anode communities were dominated by Clostridia. These results suggest that the presence of organic carbon substrate (acetate) was not the major limiting factor in selecting for highly electrogenic bacterial communities, while the quality of available organic matter may have played a significant role in supporting high performing bacterial communities.

Planktonic microbes in the Gulf of Maine area

In the Gulf of Maine area (GoMA), as elsewhere in the ocean, the organisms of greatest numerical abundance are microbes. Viruses in GoMA are largely cyanophages and bacteriophages, including podoviruses which lack tails. There is also evidence of Mimivirus and Chlorovirus in the metagenome. Bacteria in GoMA comprise the dominant SAR11 phylotype cluster, and other abundant phylotypes such as SAR86-like cluster, SAR116-like cluster, Roseobacter, Rhodospirillaceae, Acidomicrobidae, Flavobacteriales, Cytophaga, and unclassified Alphaproteobacteria and Gammaproteobacteria clusters. Bacterial epibionts of the dinoflagellate Alexandrium fundyense include Rhodobacteraceae, Flavobacteriaceae, Cytophaga spp., Sulfitobacter spp., Sphingomonas spp., and unclassified Bacteroidetes. Phototrophic prokaryotes in GoMA include cyanobacteria that contain chlorophyll (mainly Synechococcus), aerobic anoxygenic phototrophs that contain bacteriochlorophyll, and bacteria that contain proteorhodopsin. Eukaryotic microalgae in GoMA include Bacillariophyceae, Dinophyceae, Prymnesiophyceae, Prasinophyceae, Trebouxiophyceae, Cryptophyceae, Dictyochophyceae, Chrysophyceae, Eustigmatophyceae, Pelagophyceae, Synurophyceae, and Xanthophyceae. There are no records of Bolidophyceae, Aurearenophyceae, Raphidophyceae, and Synchromophyceae in GoMA. In total, there are records for 665 names and 229 genera of microalgae. Heterotrophic eukaryotic protists in GoMA include Dinophyceae, Alveolata, Apicomplexa, amoeboid organisms, Labrynthulida, and heterotrophic marine stramenopiles (MAST). Ciliates include Strombidium, Lohmaniella, Tontonia, Strobilidium, Strombidinopsis and the mixotrophs Laboea strobila and Myrionecta rubrum (ex Mesodinium rubra). An inventory of selected microbial groups in each of 14 physiographic regions in GoMA is made by combining information on the depth-dependent variation of cell density and the depth-dependent variation of water volume. Across the entire GoMA, an estimate for the minimum abundance of cell-based microbes is 1.7×10²⁵ organisms. By one account, this number of microbes implies a richness of 10⁵ to 10⁶ taxa in the entire water volume of GoMA. Morphological diversity in microplankton is well-described but the true extent of taxonomic diversity, especially in the femtoplankton, picoplankton and nanoplankton – whether autotrophic, heterotrophic, or mixotrophic, is unknown.

Links between archaeal community structure, vegetation type and methanogenic pathway in Alaskan peatlands

Although northern peatlands contribute significantly to natural methane emissions, recent studies of the importance and type of methanogenesis in these systems have provided conflicting results. Mechanisms controlling methanogenesis in northern peatlands remain poorly understood, despite the importance of methane as a greenhouse gas. We used 16S rRNA gene retrieval and denaturing gradient gel electrophoresis (DGGE) to analyse archaeal communities in 15 high-latitude peatland sites in Alaska and three mid-latitude peatland sites in Massachusetts. Archaeal community composition was analysed in the context of environmental, vegetation and biogeochemical factors characterized in a parallel study. Phylogenetic analysis revealed that Alaskan sites were dominated by a cluster of uncultivated crenarchaeotes and members of the families Methanomicrobiaceae and Methanobacteriaceae, which are not acetoclastic. Members of the acetoclastic family Methanosarcinaceae were not detected, whereas those of the family Methanosaetaceae were either not detected or were minor. These results are consistent with biogeochemical evidence that acetoclastic methanogenesis is not a predominant terminal decomposition pathway in most of the sites analysed. Ordination analyses indicated a link between vegetation type and archaeal community composition, suggesting that plants (and/or the environmental conditions that control their distribution) influence both archaeal community activity and dynamics.

Chemical stress induced by copper: examination of a biofilm system

Biofilm systems have been widely used in wastewater treatment plants. However, little information is available on the impact of toxic chemicals on the performance of fixed film systems. This study was aimed at evaluating the impact of copper on a biofilm system by examining a variety of parameters, including reactor pH, DO, substrate concentrations, secretion of extracellular polymeric substances (EPS), and copper removal and accumulation. The microbial communities in the biofilms were also examined using automated ribosomal intergenic spacer analysis (ARISA). Four rotating drum biofilm reactors were used to produce biofilms. One reactor was used to produce biofilms under copper free conditions; while the others were used to produce biofilms grown under three different copper contamination levels, namely 100 ppb, 200 ppb, and 500 ppb, for a prolonged period. The following results were obtained: (1) biofilm reactor performance was not significantly impacted as demonstrated by the pH, DO, substrate removal, and total solids in the effluent; (2) however, copper contamination inhibited EPS production in the biofilms; (3) copper removal efficiencies of 25-31% were obtained for the three copper contamination levels studied; (4) fixed films functionalized as a reservoir to accumulate more copper over time; and (5) copper contamination selected for specific species that were able to tolerate this stress and that may contribute to its remediation.

Phylogenetic diversity and specificity of bacteria closely associated with Alexandrium spp. and other phytoplankton

While several studies have suggested that bacterium-phytoplankton interactions have the potential to dramatically influence harmful algal bloom dynamics, little is known about how bacteria and phytoplankton communities interact at the species composition level. The objective of the current study was to determine whether there are specific associations between diverse phytoplankton and the bacteria that co-occur with them. We determined the phylogenetic diversity of bacterial assemblages associated with 10 Alexandrium strains and representatives of the major taxonomic groups of phytoplankton in the Gulf of Maine. For this analysis we chose xenic phytoplankton cultures that (i) represented a broad taxonomic range, (ii) represented a broad geographic range for Alexandrium spp. isolates, (iii) grew under similar cultivation conditions, (iv) had a minimal length of time since the original isolation, and (v) had been isolated from a vegetative phytoplankton cell. 16S rRNA gene fragments of most Bacteria were amplified from DNA extracted from cultures and were analyzed by denaturing gradient gel electrophoresis and sequencing. A greater number of bacterial species were shared by different Alexandrium cultures, regardless of the geographic origin, than by Alexandrium species and nontoxic phytoplankton from the Gulf of Maine. In particular, members of the Roseobacter clade showed a higher degree of association with Alexandrium than with other bacterial groups, and many sequences matched sequences reported to be associated with other toxic dinoflagellates. These results provide evidence for specificity in bacterium-phytoplankton associations.

Links between phytoplankton and bacterial community dynamics in a coastal marine environment

Bacteria and phytoplankton dynamics are thought to be closely linked in coastal marine environments, with correlations frequently observed between bacterial and phytoplankton biomass. In contrast, little is known about how these communities interact with each other at the species composition level. The purpose of the current study was to analyze bacterial community dynamics in a productive, coastal ecosystem and to determine whether they were related to phytoplankton community dynamics. Near-surface seawater samples were collected in February, May, July, and September 2000 from several stations in the Bay of Fundy. Savin et al. (M.C. Savin et al., Microb Ecol 48: 51-65) analyzed the phytoplankton community in simultaneously collected samples. The attached and free-living bacterial communities were collected by successive filtration onto 5 microm and 0.22 microm pore-size filters, respectively. DNA was extracted from filters and bacterial 16S rRNA gene fragments were amplified and analyzed by denaturing gradient gel electrophoresis (DGGE). DGGE revealed that diversity and temporal variability were lower in the free-living than the attached bacterial community. Both attached and free-living communities were dominated by members of the Roseobacter and Cytophaga groups. Correspondence analysis (CA) ordination diagrams showed similar patterns for the phytoplankton and attached bacterial communities, indicating that shifts in the species composition of these communities were linked. Similarly, canonical CA revealed that the diversity, abundance, and percentage of diatoms in the phytoplankton community accounted for a significant amount of the variability in the attached bacterial community composition. In contrast, ordination analyses did not reveal an association between free-living bacteria and phytoplankton. These results suggest that there are specific interactions between phytoplankton and the bacteria attached to them, and that these interactions influence the composition of both communities.

Stimulation of Alexandrium fundyense growth by bacterial assemblages from the Bay of Fundy

AIMS

To evaluate the influence of marine bacterial assemblages from the Bay of Fundy on Alexandrium fundyense str. CB301 growth.

METHODS AND RESULTS

Bacterial assemblages were collected from the Bay of Fundy during an Alexandrium spp. bloom, serially diluted to extinction and inoculated into axenic CB301 cultures. Bacterial assemblages dramatically enhanced CB301 growth. Retrieval and analysis of 16S rDNA fragments revealed an Alteromonas sp. strain to be the only detectable bacterium in all assemblages that promoted A. fundyense and the sole bacterium found in the most dilute inoculum that promoted A. fundyense. While this bacterium has not yet been isolated, other isolates obtained from the assemblages did not stimulate A. fundyense, indicating that the observed stimulation was not a general effect of marine bacteria.

CONCLUSIONS

Bay of Fundy marine bacterial assemblages dominated by a member of the family Alteromonadaceae were found to dramatically stimulate growth of A. fundyense.

SIGNIFICANCE AND IMPACT OF THE STUDY

These results show that native bacteria have the potential to dramatically promote the growth of A. fundyense and may play an important role in influencing A. fundyense dynamics in the Bay of Fundy.

Microbial communities associated with anaerobic benzene degradation in a petroleum-contaminated aquifer

Microbial community composition associated with benzene oxidation under in situ Fe(III)-reducing conditions in a petroleum-contaminated aquifer located in Bemidji, Minn., was investigated. Community structure associated with benzene degradation was compared to sediment communities that did not anaerobically oxidize benzene which were obtained from two adjacent Fe(III)-reducing sites and from methanogenic and uncontaminated zones. Denaturing gradient gel electrophoresis of 16S rDNA sequences amplified with bacterial or Geobacteraceae-specific primers indicated significant differences in the composition of the microbial communities at the different sites. Most notable was a selective enrichment of microorganisms in the Geobacter cluster seen in the benzene-degrading sediments. This finding was in accordance with phospholipid fatty acid analysis and most-probable-number-PCR enumeration, which indicated that members of the family Geobacteraceae were more numerous in these sediments. A benzene-oxidizing Fe(III)-reducing enrichment culture was established from benzene-degrading sediments and contained an organism closely related to the uncultivated Geobacter spp. This genus contains the only known organisms that can oxidize aromatic compounds with the reduction of Fe(III). Sequences closely related to the Fe(III) reducer Geothrix fermentans and the aerobe Variovorax paradoxus were also amplified from the benzene-degrading enrichment and were present in the benzene-degrading sediments. However, neither G. fermentans nor V. paradoxus is known to oxidize aromatic compounds with the reduction of Fe(III), and there was no apparent enrichment of these organisms in the benzene-degrading sediments. These results suggest that Geobacter spp. play an important role in the anaerobic oxidation of benzene in the Bemidji aquifer and that molecular community analysis may be a powerful tool for predicting a site's capacity for anaerobic benzene degradation.

Phylogenetic and physiological diversity of sulphate-reducing bacteria isolated from a salt marsh sediment

The phylogenetic and physiological diversity of sulphate-reducing bacteria inhabiting a salt marsh rhizosphere were investigated. Sulphate-reducing bacteria were isolated from a salt marsh rhizosphere using enrichment cultures with electron donors thought to be prevalent in the rhizosphere of Spartina alterniflora. The relationship between phylogeny and nutritional characteristics of 10 strains was investigated. None of the isolates had 16S rRNA sequences identical to other delta subclass sulphate-reducers, sharing 85.3 to 98.1% sequence similarity with 16S rRNA sequences of their respective closest relatives. Phylogenetic analysis placed two isolates, obtained with ethanol as an electron donor, within the Desulfovibrionaceae. Seven isolates, obtained with acetate, butyrate, propionate, or benzoate, were placed within the Desulfobacteriaceae. One isolate, obtained with butyrate, fell within the Desulfobulbus assemblage, which is currently considered part of the Desulfobacteriaceae family. However, due to the phylogenetic breadth and physiological traits of this group, we propose that it be considered a new family, the "Desulfobulbusaceae." The isolates utilised an array of electron donors similar to their closest relatives with a few exceptions. As a whole, the phylogenetic and physiological data indicate isolation of several sulphate-reducing bacteria which might be considered as new species and representative of new genera. Comparison of the Desulfobacteriaceae isolates' 16S rRNA sequences to environmental clones originating from the same study site revealed that none shared more than 86% sequence similarity. The results provide further insight into the diversity of sulphate-reducing bacteria inhabiting the salt marsh ecosystem, as well as supporting general trends in the phylogenetic coherence of physiological traits of delta Proteobacteria sulphate reducers.

Seasonal changes in the relative abundance of uncultivated sulfate-reducing bacteria in a salt marsh sediment and in the rhizosphere of Spartina alterniflora

Phylogenetic diversity and community composition of sulfate-reducing bacteria in a salt marsh sediment and in the rhizosphere of Spartina alterniflora were investigated. Uncultivated Desulfobacteriaceae family-related phylotypes were studied by selectively amplifying 16S rRNA gene fragments from DNA extracted from salt marsh rhizosphere samples. Two novel phylotypes were retrieved from rhizosphere samples, with A01 having 89.1% sequence similarity with Desulfococcus multivorans and 4D19 having 96.3% sequence similarity with Desulfosarcina variabilis. Additionally, six sequences that were extremely closely related to Desulfococcus multivorans (99% sequence similarity) were found. Reference RNAs containing sequences identical to corresponding cloned regions of A01 or 4D19 16S rRNA were synthesized via in vitro transcription and were used in subsequent quantitative membrane hybridization experiments. Oligonucleotide probes A01-183 and 4D19-189 were designed to specifically target these two novel phylotypes and were tested for target specificity against synthesized RNA and reference RNAs extracted from pure cultures. The newly designed probes were then used, together with eubacterial probes, to determine the relative abundances of the novel phylotypes in the salt marsh sediment and the rhizosphere. Mean relative abundances of A01-183 and 4D19-189 targets were 7.5 and 3.4%, respectively, suggesting that the target organisms of A01-183 and, to a lesser extent, of 4D19-189 play an important role in the salt marsh sediment and the Spartina rhizosphere. A seasonal trend of increased A01 relative abundance during the period of vegetative plant growth was evident, suggesting a close interaction between A01 and S. alterniflora.