Deep-Sea Archaea Fix and Share Nitrogen in Methane-Consuming Microbial Consortia

Nitrogen-fixing (diazotrophic) microorganisms regulate productivity in diverse ecosystems; however, the identities of diazotrophs are unknown in many oceanic environments. Using single-cell–resolution nanometer secondary ion mass spectrometry images of ^(15)N incorporation, we showed that deep-sea anaerobic methane-oxidizing archaea fix N_2, as well as structurally similar CN^–, and share the products with sulfate-reducing bacterial symbionts. These archaeal/bacterial consortia are already recognized as the major sink of methane in benthic ecosystems, and we now identify them as a source of bioavailable nitrogen as well. The archaea maintain their methane oxidation rates while fixing N_2 but reduce their growth, probably in compensation for the energetic burden of diazotrophy. This finding extends the demonstrated lower limits of respiratory energy capable of fueling N_2 fixation and reveals a link between the global carbon, nitrogen, and sulfur cycles

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

Algae and Clay Water Additives Differentially Impact Survival and Microbial Community Structure in Sablefish (Anoplopoma fimbria) Rearing Tanks

Algae, or “greenwater,” is a traditional water additive used in finfish aquaculture but it is associated with high costs and potentially harmful bacterial growth. “Claywater,” a mix of clay and seawater, has been explored as a replacement for greenwater. In some fish species, however, claywater reduces survival rates, but the mechanisms are not understood. A link between water additive and microbial community composition may exist. In this study, the effects of different water additives on the microbial communities of larval sablefish were studied. Three treatments were evaluated: a traditional greenwater additive, a claywater additive, and a greenwater additive switched to claywater after 1 week. Microbial communities were characterized using 16S rRNA gene sequencing, and sablefish survival and growth were recorded. Tank seawater microbial communities were significantly influenced by water additive (treatment). Sablefish microbiomes were significantly but weakly influenced by treatment, and there were time-specific differences within the claywater treatment. Sablefish, from the treatment that was switched after 1 week, maintained microbiomes that were more similar to the initial greenwater treatment. In general, sablefish were dominated by Vibrionaceae operational taxonomic units (OTUs). Variability in the sablefish microbiomes between tanks from the same treatment was high, especially in the claywater treatment, which may have confounded treatment effects. Larvae in the claywater treatment had significantly lower survival rates compared to greenwater and greenwater-claywater treatments, but no treatment effect was observed on sablefish growth (length). Overall, results suggest that claywater does not negatively impact survival or the microbial community of sablefish when preceded by 1 week of greenwater

Ultraviolet disinfection impacts the microbial community composition and function of treated wastewater effluent and the receiving urban river

Background In the United States, an estimated 14,748 wastewater treatment plants (WWTPs) provide wastewater collection, treatment, and disposal service to more than 230 million people. The quality of treated wastewater is often assessed by the presence or absence of fecal indicator bacteria. UV disinfection of wastewater is a common final treatment step used by many wastewater treatment plants in order to reduce fecal coliform bacteria and other pathogens; however, its potential impacts on the total effluent bacterial community are seemingly varied. This is especially important given that urban WWTPs typically return treated effluent to coastal and riverine environments and thus are a major source of microorganisms, genes, and chemical compounds to these systems. Following rainfall, stormflow conditions can result in substantial increases to effluent flow into combined systems. Methods Here, we conducted a lab-scale UV disinfection on WWTP effluent using UV dosage of 100 mJ/cm2 and monitored the active microbiome in UV-treated effluent and untreated effluent over the course of 48 h post-exposure using 16S rRNA sequencing. In addition, we simulated stormflow conditions with effluent UV-treated and untreated effluent additions to river water and compared the microbial communities to those in baseflow river water. We also tracked the functional profiles of genes involved in tetracycline resistance (tetW) and nitrification (amoA) in these microcosms using RT-qPCR. Results We showed that while some organisms, such as members of the Bacteroidetes, are inhibited by UV disinfection and overall diversity of the microbial community decreases following treatment, many organisms not only survive, but remain active. These include common WWTP-derived organisms such as Comamonadaceae and Pseudomonas. When combined with river water to mimic stormflow conditions, these organisms can persist in the environment and potentially enhance microbial functions such as nitrification and antibiotic resistance