Constraints on mechanisms and rates of anaerobic oxidation of methane by microbial consortia: process-based modeling of ANME-2 archaea and sulfate reducing bacteria interactions

Anaerobic oxidation of methane (AOM) is the main process responsible for the removal of methane generated in Earth's marine subsurface environments. However, the biochemical mechanism of AOM remains elusive. By explicitly resolving the observed spatial arrangement of methanotrophic archaea and sulfate reducing bacteria found in consortia mediating AOM, potential intermediates involved in the electron transfer between the methane oxidizing and sulfate reducing partners were investigated via a consortium-scale reaction transport model that integrates the effect of diffusional transport with thermodynamic and kinetic controls on microbial activity. Model simulations were used to assess the impact of poorly constrained microbial characteristics such as minimum energy requirements to sustain metabolism and cell specific rates. The role of environmental conditions such as the influence of methane levels on the feasibility of H<sub>2</sub>, formate and acetate as intermediate species, and the impact of the abundance of intermediate species on pathway reversal were examined. The results show that higher production rates of intermediates via AOM lead to increased diffusive fluxes from the methane oxidizing archaea to sulfate reducing bacteria, but the build-up of the exchangeable species can cause the energy yield of AOM to drop below that required for ATP production. Comparison to data from laboratory experiments shows that under the experimental conditions of Nauhaus et al. (2007), none of the potential intermediates considered here is able to support metabolic activity matching the measured rates

Bt176 corn in poultry nutrition: physiological characteristics and fate of recombinant plant DNA in chickens

A genetically modified Bt176 corn hybrid, which contains an insecticidal protein against the European corn borer, and its conventional, nonmodified counterpart were evaluated in 4 separate trials to verify substantial equivalence in feeding value and animal performance. Thirty-six individually kept laying hens and 3 replicates of 94 broiler chickens each, assigned to 12 cages, were fed 2 different hen and broiler diets containing either 60% conventional or 60% Bt176 corn. The nutrient compositions of the 2 corn hybrids and the 2 corn diets revealed no major differences. Furthermore, metabolism and performance data revealed no significant differences between the birds that received the conventional, nonmodified corn, and those that received the modified corn diets. The detection of the genetic modification, by PCR, in feed obtained from insect-resistant Bt corn, in tissues and products from animals fed Bt corn is described. In all evaluated chicken tissues of muscle, liver, and spleen, the corn-chloroplast ivr gene fragment was amplified. It can be deduced from these findings and from other studies that the transfer of DNA fragments into the body is a normal process that takes place constantly. Nevertheless, no recombinant plant DNA fragments such as recombinant bla or cry1A(b) fragments could be found. Bt-gene specific constructs from the Bt corn were not detected in any of the poultry samples, neither in organs, meat, nor egg

Role of bacterial isolates in enhancing the bud induction in the industrially important red alga Gracilaria dura

Plant growth depends on the integration of environmental cues, nitrogen fixation and phytohormone-signaling pathways. The growth and development of Gracilaria dura was significantly influenced by the association of bacterial isolates. The putative bud-inducing epiphytic Exiguobacterium homiense and endophytic Bacillus pumilus, Bacillus licheniformis were examined for their ability to fix nitrogen and produce indole-3-acetic acid (IAA). These bacterial isolates were identified to the species level by biochemical tests, fatty acid and partial 16S rRNA gene sequence analysis. The B. pumilus, B. licheniformis and E. homiense produced 445.5, 335 and 184.1 μg mL−1 IAA and 12.51, 10.14 and 6.9 mM mL−1 ammonium, respectively, as determined using HPLC and spectroscopy. New bud regeneration observed after the addition of total protein of the bacterial isolates suggests that IAA is conjugated with protein. The epi- and endophytic bacterial isolates were able to induce five and 10 new buds per frond, respectively, in comparison to the control, where one to two buds were observed. The combination of 25 °C and 30‰ showed the optimum condition for bud induction in G. dura when incubated with the total protein of B. pumilus. Our finding revealed for the first time that IAA coupled with nitrogen fixation induce and regenerate new buds in G. dur

Construction and characterization of Enterococcus faecalis CG110/gfp/pRE25*, a tool for monitoring horizontal gene transfer in complex microbial ecosystems

Enterococci are among the most notorious bacteria involved in the spread of antibiotic resistance (ABR) determinants via horizontal gene transfer, a process that leads to increased prevalence of antibiotic-resistant bacteria. In complex microbial communities with a high background of ABR genes, detection of gene transfer is possible only when the ABR determinant is marked. Therefore, the conjugative multiresistance plasmid pRE25, originating from a sausage-associated Enterococcus faecalis, was tagged with a 34-bp random sequence marker spliced by tet(M). The plasmid constructed, designated pRE25*, was introduced into E. faecalis CG110/gfp, a strain containing a gfp gene as chromosomal marker. The plasmid pRE25* is fully functional compared with its parental pRE25, occurs at one to two copies per chromosome, and can be transferred to Listeria monocytogenes and Listeria innocua at frequencies of 6 × 10−6 to 8 × 10−8 transconjugants per donor. The markers on the chromosome and the plasmid enable independent quantification of donor and plasmid, even if ABR genes occur at high numbers in the background ecosystem. Both markers were stable for at least 200 generations, permitting application of the strain in long-running experiments. Enterococcus faecalis CG110/gfp/pRE25* is a potent tool for the investigation of horizontal ABR gene transfer in complex environments such as food matrices, biofilms or colonic model

Risk management and communication in informal dairy sector in Côte d’Ivoire: Options for sustainable livelihoods

Intervention in food and nutrition was the best investment for our collective future in terms of managing co-morbidity in population. This investment should combine agricultural system with health and education. Fermented dairy products (FDP) played an important role for prolonged shelf life, microbial safety and nutrition. FDP was proved to be contaminated in Kenya, Somalia, Mali and Côte d'Ivoire by foodborne pathogens including Staphylococcus aureus and Escherichia coli. Recently, it was showed that FDP was predominated by a novel Streptococcus infantarius subsp. infantarius (Sii) variant. Sii-produced bacteriocin and fermentation activity could contribute to the suppression of pathogens and possibly mitigate socioeconomic and health risks. However, Sii as member of Streptococcus bovis group was associated with human and animal infections. Therefore, a potential application of Sii as adapted African starter culture for enhanced food safety required a thorough safety assessment. In order to improve hygiene and quality as well as to increase production for school canteens, urban consumption and sustainable livelihoods, a cross-sectional study was conducted in Korhogo (Côte d’Ivoire) from May to August 2014. The objective was to assess local technologies and the dairy value chain in relation to Sii prevalence, followed by a participatory stakeholder workshop to validate findings and derive adapted interventions. The study showed that the dairy value chain contributed to livelihoods and household income. About 90% of milk produced (range: 12-44 liters/collector) were sold via collectors, generating 6-20 Euros per day shared among herder, collector and vendor. The remaining 10% were consumed within the household. However, dairy production was low and scattered due to informal practices resulting in poor quality product. Basic hygiene such as cleaning, washing, disinfecting was lacking. Milk quality depreciated with the local practices, access to clean water and energy. Future interventions identified by stakeholders comprised (i) awareness on local dairy hygiene and nutritional value for the population especially school children, (ii) stakeholders organization around cooperative to develop sustainable dairy model (public dairy with private management); (iii) promote healthy milk products for school canteen programme in Korhogo through adapted local dairy technology

CompLaB v1.0: a scalable pore-scale model for flow, biogeochemistry, microbial metabolism, and biofilm dynamics

Microbial activity and chemical reactions in porous media depend on the local conditions at the pore scale and can involve complex feedback with fluid flow and mass transport. We present a modeling framework that quantitatively accounts for the interactions between the bio(geo)chemical and physical processes and that can integrate genome-scale microbial metabolic information into a dynamically changing, spatially explicit representation of environmental conditions. The model couples a lattice Boltzmann implementation of Navier–Stokes (flow) and advection–diffusion-reaction (mass conservation) equations. Reaction formulations can include both kinetic rate expressions and flux balance analysis, thereby integrating reactive transport modeling and systems biology. We also show that the use of surrogate models such as neural network representations of in silico cell models can speed up computations significantly, facilitating applications to complex environmental systems. Parallelization enables simulations that resolve heterogeneity at multiple scales, and a cellular automaton module provides additional capabilities to simulate biofilm dynamics. The code thus constitutes a platform suitable for a range of environmental, engineering and – potentially – medical applications, in particular ones that involve the simulation of microbial dynamics.</p

The evolution of early diagenetic processes at the Mozambique margin during the last glacial-interglacial transition

The Mozambique continental margin experienced large variations in sedimentation rates, primarily due to re-routing of sediment deposition from the Zambezi River during the last glacial-Holocene transition. As changes in sediment accumulation and organic matter deposition impose a strong control on the formation of authigenic minerals in the sediment, the distribution of these minerals may reflect the regional paleoenvironmental and paleoclimatic evolution. Combining geochemical analyses of porewaters and sediments with a reactive transport modeling approach, we reconstruct the depositional history and its effect on pyrite formation and other biogeochemical transformations at a site on the Mozambique margin over the past 27 kyr. Fitting the model to match the observed geochemical patterns, most importantly authigenic pyrite, allowed for the reconstruction of past sulfate-methane transition zone depth, which migrated in response to changes in the sediment accumulation and organic matter deposition. Changes in sediment deposition quickly affected organoclastic sulfate reduction and associated pyrite formation, but the effect on anaerobic methane oxidation and subsequent pyrite formation occurred with a lag on the order of thousands of years. Model results reveal a transition from high diagenetic reaction rates representative of near-shore depositional environments during the late glacial maximum, to a setting typical of offshore sediments with low reaction rates at the present day. Notably, the remnants of methane and dissolved iron pools produced in the past still shape the diagenetic processes at and below the sulfate-methane transition zone today. Since deglacial shelf-flooding and corresponding changes in sediment deposition occurred along continental margins worldwide, our analysis highlights the important role of non-steady state diagenesis in continental margin sediments and its relevance for paleoceanographic interpretation of sediment cores experiencing strong variations in sediment input

Co-directional replication-transcription conflicts lead to replication restart

August 24, 2011Head-on encounters between the replication and transcription machineries on the lagging DNA strand can lead to replication fork arrest and genomic instability1, 2. To avoid head-on encounters, most genes, especially essential and highly transcribed genes, are encoded on the leading strand such that transcription and replication are co-directional. Virtually all bacteria have the highly expressed ribosomal RNA genes co-directional with replication3. In bacteria, co-directional encounters seem inevitable because the rate of replication is about 10–20-fold greater than the rate of transcription. However, these encounters are generally thought to be benign2, 4, 5, 6, 7, 8, 9. Biochemical analyses indicate that head-on encounters10 are more deleterious than co-directional encounters8 and that in both situations, replication resumes without the need for any auxiliary restart proteins, at least in vitro. Here we show that in vivo, co-directional transcription can disrupt replication, leading to the involvement of replication restart proteins. We found that highly transcribed rRNA genes are hotspots for co-directional conflicts between replication and transcription in rapidly growing Bacillus subtilis cells. We observed a transcription-dependent increase in association of the replicative helicase and replication restart proteins where head-on and co-directional conflicts occur. Our results indicate that there are co-directional conflicts between replication and transcription in vivo. Furthermore, in contrast to the findings in vitro, the replication restart machinery is involved in vivo in resolving potentially deleterious encounters due to head-on and co-directional conflicts. These conflicts probably occur in many organisms and at many chromosomal locations and help to explain the presence of important auxiliary proteins involved in replication restart and in helping to clear a path along the DNA for the replisome.Biotechnology and Biological Sciences Research Council (Great Britain) (Grant BB/E006450/1)Wellcome Trust (London, England) (Grant 091968/Z/10/Z)National Institutes of Health (U.S.) (Grant GM41934)National Institutes of Health (U.S.) (Postdoctoral Fellowship GM093408)Biotechnology and Biological Sciences Research Council (Great Britain) (Sabbatical Visit

Quantifying bioirrigation using ecological parameters: a stochastic approach†

Irrigation by benthic macrofauna has a major influence on the biogeochemistry and microbial community structure of sediments. Existing quantitative models of bioirrigation rely primarily on chemical, rather than ecological, information and the depth-dependence of bioirrigation intensity is either imposed or constrained through a data fitting procedure. In this study, stochastic simulations of 3D burrow networks are used to calculate mean densities, volumes and wall surface areas of burrows, as well as their variabilities, as a function of sediment depth. Burrow networks of the following model organisms are considered: the polychaete worms Nereis diversicolor and Schizocardium sp., the shrimp Callianassa subterranea, the echiuran worm Maxmuelleria lankesteri, the fiddler crabs Uca minax, U. pugnax and U. pugilator, and the mud crabs Sesarma reticulatum and Eurytium limosum. Consortia of these model organisms are then used to predict burrow networks in a shallow water carbonate sediment at Dry Tortugas, FL, and in two intertidal saltmarsh sites at Sapelo Island, GA. Solute-specific nonlocal bioirrigation coefficients are calculated from the depth-dependent burrow surface areas and the radial diffusive length scale around the burrows. Bioirrigation coefficients for sulfate obtained from network simulations, with the diffusive length scales constrained by sulfate reduction rate profiles, agree with independent estimates of bioirrigation coefficients based on pore water chemistry. Bioirrigation coefficients for O(2 )derived from the stochastic model, with the diffusion length scales constrained by O(2 )microprofiles measured at the sediment/water interface, are larger than irrigation coefficients based on vertical pore water chemical profiles. This reflects, in part, the rapid attenuation with depth of the O(2 )concentration within the burrows, which reduces the driving force for chemical transfer across the burrow walls. Correction for the depletion of O(2 )in the burrows results in closer agreement between stochastically-derived and chemically-derived irrigation coefficient profiles