Should we build "obese" or "lean" anaerobic digesters?

Conventional anaerobic digesters (ADs) treating dairy manure are fed with raw or fermented manure rich in volatile fatty acids (VFAs). In contrast, pre-fermented AD (PF-AD) is fed with the more recalcitrant, fiber-rich fraction of manure that has been pre-fermented and depleted of VFAs. Thus, the substrate of PF-AD may be likened to a lean diet rich in fibers while the pre-fermentation stage fermenter is fed a relatively rich diet containing labile organic substances. Previous results have shown that conventional and pre-fermented ADs fed with raw or pre-fermented manure, respectively, produced comparable methane yields. The primary objective of this study was to characterize, using next-generation DNA sequencing, the bacterial communities in various bioreactors (pre-fermentation stage fermenter; various operational arrangements PF-AD; conventional single-stage AD; and a full scale AD) and compare the Firmicutes to Bacteroidetes (F/B) ratios in these different systems. Firmicutes and Bacteroidetes constituted the two most abundant phyla in all AD samples analyzed, as well as most of the samples analyzed in the fermenters and manure samples. Higher relative abundance of Bacteroidetes, ranging from 26% to 51% of bacteria, tended to be associated with PF-AD samples, while the highest relative abundance of Firmicutes occurred in the fermenter (maximum of 76% of bacteria) and manure (maximum of 66% of bacteria) samples. On average, primary stage fermenters exhibited microbiological traits linked to obesity: higher F/B ratios and a 'diet' that is less fibrous and more labile compared to that fed to PF-AD. On the other hand, microbial characteristics associated with leanness (lower F/B ratios combined with fibrous substrate) were associated with PF-AD. We propose that bacterial communities in AD shift depending on the quality of substrate, which ultimately results in maintaining VFA yields in PF-AD, similar to the role of bacterial communities and a high fiber diet in lean mice.

Ammonia-oxidizing archaea and nitrite-oxidizing nitrospiras in the biofilter of a shrimp recirculating aquaculture system.

This study analysed the nitrifier community in the biofilter of a zero discharge, recirculating aquaculture system (RAS) for the production of marine shrimp in a low density (low ammonium production) system. The ammonia-oxidizing populations were examined by targeting 16S rRNA and amoA genes of ammonia-oxidizing bacteria (AOB) and archaea (AOA). The nitrite-oxidizing bacteria (NOB) were investigated by targeting the 16S rRNA gene. Archaeal amoA genes were more abundant in all compartments of the RAS than bacterial amoA genes. Analysis of bacterial and archaeal amoA gene sequences revealed that most ammonia oxidizers were related to Nitrosomonas marina and Nitrosopumilus maritimus. The NOB detected were related to Nitrospira marina and Nitrospira moscoviensis, and Nitrospira marina-type NOB were more abundant than N. moscoviensis-type NOB. Water quality and biofilm attachment media played a role in the competitiveness of AOA over AOB and Nitrospira marina-over N. moscoviensis-type NOB.

The secrets of El Dorado viewed through a microbial perspective.

The formation of the Amazon Dark Earths was a model of sustainable soil management that involved intensive composting and charcoal (biochar) application. Biochar has been the focus of increasing research attention for carbon sequestration, although the role of compost or humic substances (HS) as they interact with biochar has not been much studied. We provide a perspective that biochar and HS may facilitate extracellular electron transfer (EET) reactions in soil, which occurs under similar conditions that generate the greenhouse gases methane and nitrous oxide. Facilitating EET may constitute a viable strategy to mitigate greenhouse gas emission. In general, we lack knowledge in the mechanisms that link the surface chemical characteristics of biochar to the physiology of microorganisms that are involved in various soil processes including those that influence soil organic matter dynamics and methane and nitrous oxide emissions. Most studies view biochar as a mostly inert microbial substrate that offers little other than a high sorptive surface area. Synergism between biochar and HS resulting in enhanced EET provides a mechanism to link electrochemical properties of these materials to microbial processes in sustainable soils.

Methane production on thickened, pre-fermented manure.

Over 9 million dairy cows generate an estimated 226 billion kg of wet manure annually in the US. The purpose of this study was to demonstrate the viability of a novel two-stage anaerobic digestion (AD) process for producing methane-rich biogas on pre-fermented dairy manure. In summary, it was observed that AD of thickened pre-fermented manure can generate comparable biogas quantities to AD using raw manure, with enhanced methane content. Despite receiving a lower quality (i.e., partially biodegraded) substrate, biogas stoichiometry and overall process stability in the two-stage system was also comparable to AD receiving raw manure. Finally, the two-stage AD was more enriched with the acetoclastic methanogen Methanosarcinaceae (Msc; compared to AD of raw manure) and biogas production appeared closely linked with the Msc fraction. In fact, the enhanced enrichment of Msc likely contributed to the successful and stable operations.

Thorsellia anophelis is the dominant bacterium in a Kenyan population of adult Anopheles gambiae mosquitoes.

Anopheles gambiae mosquitoes are not known to harbor endosymbiotic bacteria. Here we show, using nucleic acid-based methods, that 16S rRNA gene sequences specific to a recently described mosquito midgut bacterium, Thorsellia anophelis, is predominant in the midgut of adult An. gambiae s.l. mosquitoes captured in residences in central Kenya, and also occurs in the aquatic rice paddy environment nearby. PCR consistently detected T. anophelis in the surface microlayer of rice paddies, which is also consistent with the surface-feeding behavior of A. gambiae s.l. larvae. Phylogenetic analysis of cloned environmental 16S rRNA genes identified four major Thorsellia lineages, which are closely affiliated to an insect endosymbiont of the genus Arsenophonus. Physiological characterizations support the hypothesis that T. anophelis is well adapted to the female anopheline midgut by utilizing blood and tolerating the alkaline conditions in this environment. The results suggest that aquatically derived bacteria such as T. anophelis can persist through mosquito metamorphosis and become well-established in the adult mosquito midgut.

Microbial diversity and dynamics in multi- and single-compartment anaerobic bioreactors processing sulfate-rich waste streams.

We investigated bacterial and archaeal community structures and population dynamics in two anaerobic bioreactors processing a carbohydrate- and sulfate-rich synthetic wastewater. A five-compartment anaerobic migrating blanket reactor (AMBR) was designed to promote biomass and substrate staging, which partially separates the processes of methanogenesis and sulfidogenesis in the middle and outer compartment(s) respectively. The second reactor was a conventional, single-compartment upflow anaerobic sludge blanket (UASB) reactor. Both reactors, which were seeded with the same inoculum, performed well when the influent chemical oxygen demand (COD)/SO(4) (2-) mass ratio was 24.4. The AMBR performed worse than the UASB reactor when the influent COD/SO(4) (2-) mass ratio was decreased to 5.0 by raising the sulfate load. Terminal restriction fragment length polymorphism analyses of bacterial 16S rRNA genes showed that the increase in sulfate load had a greater impact on bacterial diversity and community structure for the five AMBR compartments than for the UASB reactor. Moreover, bacterial community profiles across AMBR compartments became more similar through time, indicating a converging, rather than a staged community. While similar populations were abundant in both reactors at the beginning of the experiment, fermenting bacteria (clostridia, streptococci), and sulfate-reducing bacteria became more abundant in the AMBR, after shifting to a higher sulfate load, while a novel Thermotogales-like population eventually became predominant in the UASB reactor. A similar shift in the community structure of the hydrogenotrophic methanogens in the AMBR occurred: representatives of the Methanobacteriaceae out-competed the Methanospirillaceae after increasing the sulfate load in the AMBR, while the archaeal community structure was maintained in the UASB.

Diversity and dynamics of microbial communities in engineered environments and their implications for process stability.

The availability of molecular biological tools for studying microbial communities in bioreactors and other engineered systems has resulted in remarkable insights linking diversity and dynamics to process stability. As engineered systems are often more manageable than large-scale ecosystems, and because parallels between engineered environments and other ecosystems exist, the former can be used to elucidate some unresolved ecological issues. For example, the process stability of methanogenic bioreactors containing well-defined trophic groups appears to depend on the diversity of the functional groups within each trophic level as well as on how these functional groups complement each other. In addition to using engineered systems to study general ecological questions, microbial ecologists and environmental engineers need to investigate conditions, processes, and interactions in engineered environments in order to make the ecological engineering of bioreactor design and operation more practicable.

Influence of different cultivars on populations of ammonia-oxidizing bacteria in the root environment of rice.

Comparisons of the activities and diversities of ammonia-oxidizing bacteria (AOB) in the root environment of different cultivars of rice (Oryza sativa L.) indicated marked differences despite identical environmental conditions during growth. Gross nitrification rates obtained by the 15N dilution technique were significantly higher in a modern variety, IR63087-1-17, than in two traditional varieties. Phylogenetic analysis based on the ammonium monooxygenase gene (amoA) identified strains related to Nitrosospira multiformis and Nitrosomonas europaea as the predominant AOB in our experimental rice system. A method was developed to determine the abundance of AOB on root biofilm samples using fluorescently tagged oligonucleotide probes targeting 16S rRNA. The levels of abundance detected suggested an enrichment of AOB on rice roots. We identified 40 to 69% of AOB on roots of IR63087-1-17 as Nitrosomonas spp., while this subpopulation constituted 7 to 23% of AOB on roots of the other cultivars. These results were generally supported by denaturing gradient gel electrophoresis of the amoA gene and analysis of libraries of cloned amoA. In hydroponic culture, oxygen concentration profiles around secondary roots differed significantly among the tested rice varieties, of which IR63087-1-17 showed maximum leakage of oxygen. The results suggest that varietal differences in the composition and activity of root-associated AOB populations may result from microscale differences in O2 availability.