Improving biochemical yields with MixoFerm

Acetyl-CoA is a primary hub for metabolism and is the building block for most biochemicals of interest. However, the yields for biochemicals derived from acety-CoA are inherently limited because of the decarboxylation of pyruvate to acetyl-CoA which releases CO2. To overcome this limitation, White Dog Labs (WDL) developed a fermentation technology call MixoFerm™ (also known as anaerobic, non-photosynthetic mixotrophy). This technology uses microorganisms capable of concurrently utilizing both organic (e.g., sugars) and inorganic (e.g., CO2) substrates. Using MixoFerm, CO2 can be fixed back into acetyl-CoA and thus improve biochemical yields (g product/g substrate consumed). Here, we demonstrate simultaneous utilization of both fructose and syngas by Clostridium ljungdahlii and Clostridium autoethanogenum. We next engineered C. ljungdahlii to produce the non-native metabolite acetone at a yield 35% greater than the theoretical maximum acetone yield without mixotrophy. Finally, we designed and generated a strain of C. ljungdahlii capable of consuming glucose, which the wild-type strain is unable to do. With the ability to improve biochemical yields, MixoFerm™ is a robust and flexible platform technology to improve process economics and product life-cycle analysi

Small RNAs in the Genus Clostridium

The genus Clostridium includes major human pathogens and species important to cellulose degradation, the carbon cycle, and biotechnology. Small RNAs (sRNAs) are emerging as crucial regulatory molecules in all organisms, but they have not been investigated in clostridia. Research on sRNAs in clostridia is hindered by the absence of a systematic method to identify sRNA candidates, thus delegating clostridial sRNA research to a hit-and-miss process. Thus, we wanted to develop a method to identify potential sRNAs in the Clostridium genus to open up the field of sRNA research in clostridia. Using comparative genomics analyses combined with predictions of rho-independent terminators and promoters, we predicted sRNAs in 21 clostridial genomes: Clostridium acetobutylicum, C. beijerinckii, C. botulinum (eight strains), C. cellulolyticum, C. difficile, C. kluyveri (two strains), C. novyi, C. perfringens (three strains), C. phytofermentans, C. tetani, and C. thermocellum. Although more than one-third of predicted sRNAs have Shine-Dalgarno (SD) sequences, only one-sixth have a start codon downstream of SD sequences; thus, most of the predicted sRNAs are noncoding RNAs. Quantitative reverse transcription-PCR (Q-RT-PCR) and Northern analysis were employed to test the presence of a randomly chosen set of sRNAs in C. acetobutylicum and several C. botulinum strains, leading to the confirmation of a large fraction of the tested sRNAs. We identified a conserved, novel sRNA which, together with the downstream gene coding for an ATP-binding cassette (ABC) transporter gene, responds to the antibiotic clindamycin. The number of predicted sRNAs correlated with the physiological function of the species (high for pathogens, low for cellulolytic, and intermediate for solventogenic), but not with 16S rRNA-based phylogeny

Production of biochemicals and biofuels with no CO2 production and improved product yields

Traditional fermentation processes for the production of the majority of biochemicals and biofuels produce CO2 because of decarboxylation reactions, which limits the final mass yields of products. To overcome this limitation, we have developed a fermentation technology called MixoFerm™ (also known as anaerobic, non-photosynthetic mixotrophy), which uses microorganisms capable of simultaneously consuming both organic (e.g., sugars) and inorganic (e.g., CO2, CO, or H2) substrates. With this technology, product mass yields for almost any biochemical or biofuel can be increased by at least 50%, and processes can be designed that result in no CO2 production. In order to achieve zero CO2 emissions for most products, exogenous reductant must be added to the system, since sugar lacks the necessary reducing energy to both fix CO2 and produce the product of interest. Here, we demonstrate concurrent consumption of both sugars and exogenously added reducing gases (CO and/or H2) to produce products of interest at enhanced mass yields and with no CO2 emissions. In addition, we have screened a library of acetogenic bacteria in order to find an optimal MixoFerm™ host strain, one that consumes both a broad range of carbohydrates and gases. From this library, we identified strains with a broader carbohydrate consumption range than traditional acetogens like C. ljungdahlii or C. autoethanogenum, and characterized their ability to grow under a variety of MixoFerm™ conditions to produce biochemicals at enhanced mass yields. With the ability to improve product yields for reduced products, especially for ethanol and other potential biofuels, MixoFerm™ is a robust and flexible platform technology to improve process economics and product life-cycle analysis

The transcriptional program underlying the physiology of clostridial sporulation

A detailed microarray analysis of transcription during sporulation of the strict anaerobe and endospore former Clostridium acetobutylicum is presented

Using plant volatile traps to estimate the diversity of natural enemy communities in orchard ecosystems

In this study we used sticky traps baited with plant volatile lures to monitor the biodiversity of natural enemies in orchard ecosystems in the western U.S. We compared the diversity of predator genera from season total trap catches in 37 different orchards (apple, cherry, pear and walnut) over a two-year period (2010−2011) using standardized Hill number biodiversity indices and community similarity profiles. For a subset of 23 of these orchards we were also able to monitor the change in biodiversity of predator genera over the full growing season in the different orchard crops. A total of 37,854 individuals from 31 different genera of foliage-active generalist predators were collected from all orchards combined. Mean sample coverage was high (0.98) and richness, diversity and evenness differed between crops in 2010, but not in 2011. There was more than 90% similarity in the richness of predator genera among crops and among orchards within crops, but a greater level of differentiation was observed among orchards when variation in their relative abundance and dominance in the communities was taken into account. There was a consistent rise in predator generic richness and diversity through the season in both years for apple, cherry and pear orchards, but in walnut orchards, a steep rise from March to May was followed by a decline through the rest of the season. In an additional component of the study, the species level similarity of predator and parasitoid communities was analyzed for total season trap catch data from six walnut orchards. The rarefied species richness of parasitoids was much greater than that for predators, although the diversity, evenness and dominance of the parasitoid species varied considerably among orchards. The results from this study highlight the fact that natural enemy communities in orchard ecosystems can be effectively monitored using plant volatile traps, and that these communities are surprisingly diverse despite frequent disturbance from pest management intervention

Sulfolipid substitution ratios of Microcystis aeruginosa and planktonic communities as an indicator of phosphorus limitation in Lake Erie

Phosphorus (P) availability frequently limits primary production in lakes, influences the physiology of phytoplankton, shapes community structure, and can stimulate or constrain the formation of cyanobacterial blooms. Given the importance of P, numerous methods are available to assess P stress in phytoplankton communities. Marine phytoplankton are known to substitute sulfolipids for phospholipids in response to P limitation. We asked whether sulfolipid substitution might serve as an additional indicator of P stress in freshwater phytoplankton communities. The question was addressed using cultures of Microcystis aeruginosa, Lake Erie microcosms, and surveys of lipid profiles in Lake Erie during a Microcystis spp. bloom. Peak area response ratios of the intact polar lipids sulfoquinovosyldiacylglycerol (SQDG) to phosphatidylglycerol (PG) were used as the metric of lipid substitution. In cultures of M. aeruginosa NIES-843, the SQDG : PG ratio increased from ~ 0.9 to ~ 3.3 with decreasing P concentration. In P-limited communities, the SQDG : PG ratio increased from ~ 6 to ~ 11 after 48 h in microcosm controls, while P amendments reduced the ratio to ~ 3. In Lake Erie surveys, the SQDG : PG ratio ranged from ~ 0.4 to ~ 7.4 and was negatively correlated (Pearson r = −0.62) with total dissolved P. The SQDG : PG ratio was not correlated with concentrations of chlorophyll a, soluble reactive P, or N : P molar ratios. These results demonstrated that M. aeruginosa and Microcystis-dominated communities remodel lipid profiles in response to P scarcity, providing a potential short-term, time-integrated biomarker of nutrient history and P stress in fresh waters

Genetic validation of bipolar disorder identified by automated phenotyping using electronic health records

Bipolar disorder (BD) is a heritable mood disorder characterized by episodes of mania and depression. Although genomewide association studies (GWAS) have successfully identified genetic loci contributing to BD risk, sample size has become a rate-limiting obstacle to genetic discovery. Electronic health records (EHRs) represent a vast but relatively untapped resource for high-throughput phenotyping. As part of the International Cohort Collection for Bipolar Disorder (ICCBD), we previously validated automated EHR-based phenotyping algorithms for BD against in-person diagnostic interviews (Castro et al. Am J Psychiatry 172:363–372, 2015). Here, we establish the genetic validity of these phenotypes by determining their genetic correlation with traditionally ascertained samples. Case and control algorithms were derived from structured and narrative text in the Partners Healthcare system comprising more than 4.6 million patients over 20 years. Genomewide genotype data for 3330 BD cases and 3952 controls of European ancestry were used to estimate SNP-based heritability (h2g) and genetic correlation (rg) between EHR-based phenotype definitions and traditionally ascertained BD cases in GWAS by the ICCBD and Psychiatric Genomics Consortium (PGC) using LD score regression. We evaluated BD cases identified using 4 EHR-based algorithms: an NLP-based algorithm (95-NLP) and three rule-based algorithms using codified EHR with decreasing levels of stringency—“coded-strict”, “coded-broad”, and “coded-broad based on a single clinical encounter” (coded-broad-SV). The analytic sample comprised 862 95-NLP, 1968 coded-strict, 2581 coded-broad, 408 coded-broad-SV BD cases, and 3 952 controls. The estimated h2g were 0.24 (p = 0.015), 0.09 (p = 0.064), 0.13 (p = 0.003), 0.00 (p = 0.591) for 95-NLP, coded-strict, coded-broad and coded-broad-SV BD, respectively. The h2g for all EHR-based cases combined except coded-broad-SV (excluded due to 0 h2g) was 0.12 (p = 0.004). These h2g were lower or similar to the h2g observed by the ICCBD + PGCBD (0.23, p = 3.17E−80, total N = 33,181). However, the rg between ICCBD + PGCBD and the EHR-based cases were high for 95-NLP (0.66, p = 3.69 × 10–5), coded-strict (1.00, p = 2.40 × 10−4), and coded-broad (0.74, p = 8.11 × 10–7). The rg between EHR-based BD definitions ranged from 0.90 to 0.98. These results provide the first genetic validation of automated EHR-based phenotyping for BD and suggest that this approach identifies cases that are highly genetically correlated with those ascertained through conventional methods. High throughput phenotyping using the large data resources available in EHRs represents a viable method for accelerating psychiatric genetic research

From planning to execution to the future: An overview of a concerted effort to enhance biological control in apple, pear, and walnut orchards in the western U.S.

We embarked on a large project designed to help enhance biological control in apple, pear and walnut orchards in the western U.S., where management programs were in the midst of a transition from older organo-phosphate insecticides to mating disruption and newer reduced-risk insecticides. A “pesticide replacement therapy” approach resulted in unstable management programs with unpredictable outbreaks of spider mites and aphids. Our project was designed to provide growers and pest managers with information on the effects of newer pesticide chemistries on a suite of representative natural enemies in both the laboratory and field, potential of new monitoring tools using herbivore-induced plant volatiles and floral volatiles, phenology of the key natural enemy species, economic consequences of using an enhanced biological control program, and value of an outreach program to get project outcomes into the hands of decision-makers. We present an overview of both the successes and failures of the project and of new projects that have spun off from this project to further enhance biological control in our systems in the near future

Seed systems smallholder farmers use

Seed can be an important entry point for promoting productivity, nutrition and resilience among smallholder farmers. While investments have primarily focused on strengthening the formal sector, this article documents the degree to which the informal sector remains the core for seed acquisition, especially in Africa. Conclusions drawn from a uniquely comprehensive data set, 9660 observations across six countries and covering 40 crops, show that farmers access 90.2 % of their seed from informal systems with 50.9 % of that deriving from local markets. Further, 55 % of seed is paid for by cash, indicating that smallholders are already making important investments in this arena. Targeted interventions are proposed for rendering formal and informal seed sector more smallholder-responsive and for scaling up positive impacts