Biogeography and Genetic Diversity of Toxin Producing Cyanobacteria in a Laurentian Great Lake

The North American Great Lakes are a vital source on a global scale, as they hold ~18 % of the potable water resources on our planet. Cyanobacteria of the genus Microcystis are commonly found in fresh water environments around the world, and since the mid-1990s also in Lake Erie. The reasons for the success for these potentially toxic cyanobacteria in Lake Erie are not completely understood. In this study we have applied modern molecular tools to analyze field samples to provide an insight into the genotypic composition and diversity of the Microcystis community in the past and present day Lake Erie. We have also analyzed a three-year data set to identify specific environmental factors that contribute to the abundance of Microcystis genotypes and microcystin production. In addition, in a laboratory-based study we examined the effect of nutrients on transcriptional activity of the microcystin synthetase gene mcyD. The results of this study suggest that, although toxic Microcystis form \u3c 10 % of the total cyanobacterial population in Lake Erie, the toxin-producing Microcystis community in Lake Erie is diverse, and that these populations are stabile on a time scale of decades. Sediments acting as a reservoir of Microcystis are likely contributing to the persistence of the population. Although Microcystis is the dominant microcystin producer in the lake, other microcystin-producing cyanobacteria were also found in spatially isolated regions of the lake. While microcystin concentration in Lake Erie is correlated positively with total phosphorus (P\u3c0.001) and surface reactive phosphorus (P\u3c0.001), and negatively with the molar ratio total nitrogen to total phosphorus (P\u3c0.001); toxic Microcystis abundance correlates negatively with NO3 concentration (P=0.04) and positively with surface water temperatures (ranging from 20.8 °C to 27.4 °C) (P=0.03). These observations, along with findings from culture based experiments, suggest decoupling of the factors governing proliferation of toxic cells and toxin production. Culture based experiments also suggested that the chemical form of phosphorus may be an important factor in regulating microcystin biosynthesis in Microcystis based on monitoring relative transcriptional activity of the mcyD gene. The transcriptional activity of mcyD was higher (P=0.118) in cells grown in BG11-medium containing 2.3 μM organic phosphorus (glycerol 2-phosphate disodium salt hydrate) than in cells grown in BG11-medium containing 2.3 μM inorganic phosphorus (K2HPO4)

Spatial variations in bacterial and archaeal abundance and community composition in boreal forest pine mycorrhizospheres

Mycorrhizal fungi have a strong impact on soil biota. In this study, bacterial and archaeal populations in different parts of Suillus bovinus - Pinus sylvestris mycorrhizospheres in boreal forest were quantified and identified by DNA analysis. The numbers of bacterial and archaeal 16S rRNA gene copies were highest in uncolonized humus and lowest in fruiting bodies. The numbers of bacterial 16S rRNA gene copies varied from 1.3 x 10(7) to 3.1 x 10(9) copies g(-1) fw and archaeal copies from 4.1 x 10(7) to 9.6 x 10(8) copies g(-1) fw. The relatively high number of archaeal 16S rRNA gene copies was likely due to the cold and highly organic habitat. The presence of hyphae appeared to further promote archaeal numbers and the archaea:bacteria ratio was over one in samples containing only fungal material. Most detected archaea belonged to terrestrial Thaumarchaeota. Proteobacteria, Actinobacteria and Acidobacteria were predictably the dominating bacterial taxa in the samples with clear trend of Betaproteobacteria preferring the pine root habitats.Peer reviewe

Spatial variations in bacterial and archaeal abundance and community composition in boreal forest pine mycorrhizospheres

Mycorrhizal fungi have a strong impact on soil biota. In this study, bacterial and archaeal populations in different parts of Suillus bovinus - Pinus sylvestris mycorrhizospheres in boreal forest were quantified and identified by DNA analysis. The numbers of bacterial and archaeal 16S rRNA gene copies were highest in uncolonized humus and lowest in fruiting bodies. The numbers of bacterial 16S rRNA gene copies varied from 1.3 × 107 to 3.1 × 109 copies g−1 fw and archaeal copies from 4.1 × 107 to 9.6 × 108 copies g−1 fw. The relatively high number of archaeal 16S rRNA gene copies was likely due to the cold and highly organic habitat. The presence of hyphae appeared to further promote archaeal numbers and the archaea:bacteria ratio was over one in samples containing only fungal material. Most detected archaea belonged to terrestrial Thaumarchaeota. Proteobacteria, Actinobacteria and Acidobacteria were predictably the dominating bacterial taxa in the samples with clear trend of Betaproteobacteria preferring the pine root habitats.acceptedVersionPeer reviewe

Analyzing Gene Expression from Marine Microbial Communities using Environmental Transcriptomics

Analogous to metagenomics, environmental transcriptomics (metatranscriptomics) retrieves and sequences environmental mRNAs from a microbial assemblage without prior knowledge of what genes the community might be expressing. Thus it provides the most unbiased perspective on community gene expression in situ. Environmental transcriptomics protocols are technically difficult since prokaryotic mRNAs generally lack the poly(A) tails that make isolation of eukaryotic messages relatively straightforward 1 and because of the relatively short half lives of mRNAs 2. In addition, mRNAs are much less abundant than rRNAs in total RNA extracts, thus an rRNA background often overwhelms mRNA signals. However, techniques for overcoming some of these difficulties have recently been developed. A procedure for analyzing environmental transcriptomes by creating clone libraries using random primers to reverse-transcribe and amplify environmental mRNAs was recently described was successful in two different natural environments, but results were biased by selection of the random primers used to initiate cDNA synthesis 3. Advances in linear amplification of mRNA obviate the need for random primers in the amplification step and make it possible to use less starting material decreasing the collection and processing time of samples and thereby minimizing RNA degradation 4. In vitro transcription methods for amplifying mRNA involve polyadenylating the mRNA and incorporating a T7 promoter onto the 3 end of the transcript. Amplified RNA (aRNA) can then be converted to double stranded cDNA using random hexamers and directly sequenced by pyrosequencing 5. A first use of this method at Station ALOHA demonstrated its utility for characterizing microbial community gene expression 6

Ex-situ biological hydrogen methanation in trickle bed reactors : Integration into biogas production facilities

Biological hydrogen methanation (BHM) is a biocatalytic process for biogas upgrading. Integrating ex-situ BHM processes into biogas facilities has the advantage of using inoculum, CO2, and nutrients directly from anaerobic digestion (AD) processes to enhance CH4 productivity. This study investigated the potential of biowaste digestate as an inoculum and digested biowaste reject water as the trickling liquid and nutrient source in thermophilic trickle bed reactors (TBRs). Use of reject water improved H2 conversion efficiency to up to 99 %, thus achieving a H2 loading rate of 10.8 LH2 L Rv-1 d-1 at a gas retention time (GRT) of 1.8 h and CH4 productivity of 2.6 L LRv-1 d-1 implying that reject water contains macronutrients beneficial to enriching hydrogenotrophic methanogens. However, at high H2 loading rates, a trace element supply was necessary to stabilize process performance. Hydrogenotrophic methanogens Methanothermobacter and Methanobacterium were selectively enriched, mainly due to the increased H2 loading rate.publishedVersionPeer reviewe

Increasing oxygen deficiency changes rare and moderately abundant bacterial communities in coastal soft sediments

Coastal hypoxia is a major environmental problem worldwide. Hypoxia-induced changes in sediment bacterial communities harm marine ecosystems and alter biogeochemical cycles. Nevertheless, the resistance of sediment bacterial communities to hypoxic stress is unknown. We investigated changes in bacterial communities during hypoxic-anoxic disturbance by artificially inducing oxygen deficiency to the seafloor for 0, 3, 7, and 48 days, with subsequent molecular biological analyses. We further investigated relationships between bacterial communities, benthic macrofauna and nutrient effluxes across the sediment-water-interface during hypoxic-anoxic stress, considering differentially abundant operational taxonomic units (OTUs). The composition of the moderately abundant OTUs changed significantly after seven days of oxygen deficiency, while the abundant and rare OTUs first changed after 48 days. High bacterial diversity maintained the resistance of the communities during oxygen deficiency until it dropped after 48 days, likely due to anoxia-induced loss of macrofaunal diversity and bioturbation. Nutrient fluxes, especially ammonium, correlated positively with the moderate and rare OTUs, including potential sulfate reducers. Correlations may reflect bacteria-mediated nutrient effluxes that accelerate eutrophication. The study suggests that even slightly higher bottom-water oxygen concentrations, which could sustain macrofaunal bioturbation, enable bacterial communities to resist large compositional changes and decrease the harmful consequences of hypoxia in marine ecosystems.Peer reviewe

Optimising nitrogen recovery from reject water in a 3-chamber bioelectroconcentration cell

With the growing demand for macronutrients, such as nitrogen, and environmental issues related to their production, there is increasing need for efficient nutrient recycling. Reject waters from the dewatering of anaerobically digested sewage sludge are potential sources for nutrient recovery due to their high ammonium nitrogen (NH4-N) concentration (ca. 1 gNH4-N L−1) and low volume (ca. 1% of incoming sewage). In this study, a 3-chamber bioelectroconcentration cell was used for NH4-N recovery into a liquid concentrate from both synthetic and real reject water. NH4-N recovery efficiency and rate were optimised based on NH4-N loading rate, varying from 1.4 to 9.4 gNH4-N L−1 d−1 with synthetic reject water. The obtained NH4-N recovery efficiencies are the highest reported to date for bioelectroconcentration, peaking at 75.5 ± 4.6% (recovery rate of 728 ± 117 gN m−3 d−1) at loading rate 1.9 gNH4-N L−1 d−1. A loading rate of 2.9 gNH4-N L−1 d−1 led to the most optimal ratio between NH4-N recovery efficiency (68.2 ± 11.6%) and recovery rate (965 ± 66 gN m−3 d−1), with NH4-N up-concentrated 7.4 ± 0.9 times to 7483 ± 625 mg L−1 in the concentrate. With real reject water, NH4-N recovery efficiency of 53.2 ± 4.0% and recovery rate of 556 ± 37 gN m−3 d−1 were obtained at loading rate 2.5 gNH4-N L−1 d−1, with a specific energy consumption of 6.1 ± 1.1 kWh kgN−1. 16S rRNA amplicon analysis showed the dominance of phyla Bacteroidetes and Firmicutes in the anodic biofilms, with a significant change in the enriched microbial communities after transitioning from synthetic to real reject water. This study indicates the potential of bioelectroconcentration for nitrogen recovery from reject water without the need for an external organic carbon source or other chemical additions.publishedVersionPeer reviewe

Acetotrophic Activity Facilitates Methanogenesis from LCFA at Low Temperatures: Screening from Mesophilic Inocula

The inoculum source plays a crucial role in the anaerobic treatment of wastewaters. Lipids are present in various wastewaters and have a high methanogenic potential, but their hydrolysis results in the production of long chain fatty acids (LCFAs) that are inhibitory to anaerobic microorganisms. Screening of inoculum for the anaerobic treatment of LCFA-containing wastewaters has been performed at mesophilic and thermophilic conditions. However, an evaluation of inocula for producing methane from LCFA-containing wastewater has not yet been conducted at low temperatures and needs to be undertaken. In this study, three inocula (one granular sludge and two municipal digester sludges) were assessed for methane production from LCFA-containing synthetic dairy wastewater (SDW) at low temperatures (10 and 20°C). A methane yield (based on mL-CH4/g-CODadded) of 86-65% with acetate and 45-20% with SDW was achieved within 10 days using unacclimated granular sludge, whereas the municipal digester sludges produced methane only at 20°C but not at 10°C even after 200 days of incubation. The acetotrophic activity in the inoculum was found to be crucial for methane production from LCFA at low temperatures, highlighting the role of Methanosaeta (acetoclastic archaea) at low temperatures. The presence of bacterial taxa from the family Syntrophaceae (Syntrophus and uncultured taxa) in the inoculum was found to be important for methane production from SDW at 10°C. This study suggests the evaluation of acetotrophic activity and the initial microbial community characteristics by high-throughput amplicon sequencing for selecting the inoculum for producing methane at low temperatures (up to 10°C) from lipid-containing wastewaters