Common principles and best practices for engineering microbiomes

Despite broad scientific interest in harnessing the power of Earth's microbiomes, knowledge gaps hinder their efficient use for addressing urgent societal and environmental challenges. We argue hat structuring research and technology developments around a design-build-test-learn (DBTL) cycle will advance microbiome engineering and spur new discoveries on the basic scientific principles governing microbiome function. In this Review, we present key elements of an iterative DBTL cycle for microbiome engineering, focusing on generalizable approaches, including top-down and bottom-up design processes, synthetic and self-assembled construction methods, and emerging tools to analyze microbiome function. These approaches can be used to harness microbiomes for broad applications related to medicine, agriculture, energy, and the environment. We also discuss key challenges and opportunities of each approach and synthesize them into best practice guidelines for engineering microbiomes. We anticipate that adoption of a DBTL framework will rapidly advance microbiome-based biotechnologies aimed at improving human and animal health, agriculture, and enabling the bioeconomy

Responsible Science, Engineering and Education for Water Resource Recovery and Circularity

Water resource recovery is central to the circular economy framework. It underlies the transition of environmental engineering from pollution prevention to responsible innovation for sustainable systems engineering. In order to speed this transition, resource recovery and circularity need integration into new higher education curricula to train the next generation of young professionals. However, training of new concepts requires the development of new course materials and books, while integrating substantial illustrations and problems on circularity and resource recovery in new editions of existing textbooks in environmental science and engineering. Moreover, university–utility–industry partnerships are important mechanisms to bridge theoretical fundamentals to concepts for engineering practice, and to promote knowledge exchange and technology adoption between practitioners and academics. Interactive platforms should be designed to facilitate the integration and development of resource recovery and circularity concepts from science and practice into education. Consensus was built on this perspective article from interaction with the members of the Association of Environmental Engineering and Science Professors in a workshop that we organized at the AEESP Research and Education Conference 2017. Overall, this paper gives actionable roadmaps to (i) apprehend how new science and technological findings need to get integrated to sustain resource recovery and circularity in practice, along with the fact that (ii) skills sets can be engineered with relatively minor changes to existing lecture material that will have maximal impact on the scope of the thought material. It lays out (iii) how partnership with engineering practitioners can make a lecture more vivid by giving students reasoning for why the learned material is important, and (iv) how a platform for an integrated science, education, and practice can deliver them with concrete tools for practical implementation for benefits at community level

Responsible Science, Engineering and Education for Water Resource Recovery and Circularity

Water resource recovery is central to the circular economy framework. It underlies the transition of environmental engineering from pollution prevention to responsible innovation for sustainable systems engineering. In order to speed this transition, resource recovery and circularity need integration into new higher education curricula to train the next generation of young professionals. However, training of new concepts requires the development of new course materials and books, while integrating substantial illustrations and problems on circularity and resource recovery in new editions of existing textbooks in environmental science and engineering. Moreover, university–utility–industry partnerships are important mechanisms to bridge theoretical fundamentals to concepts for engineering practice, and to promote knowledge exchange and technology adoption between practitioners and academics. Interactive platforms should be designed to facilitate the integration and development of resource recovery and circularity concepts from science and practice into education. Consensus was built on this perspective article from interaction with the members of the Association of Environmental Engineering and Science Professors in a workshop that we organized at the AEESP Research and Education Conference 2017. Overall, this paper gives actionable roadmaps to (i) apprehend how new science and technological findings need to get integrated to sustain resource recovery and circularity in practice, along with the fact that (ii) skills sets can be engineered with relatively minor changes to existing lecture material that will have maximal impact on the scope of the thought material. It lays out (iii) how partnership with engineering practitioners can make a lecture more vivid by giving students reasoning for why the learned material is important, and (iv) how a platform for an integrated science, education, and practice can deliver them with concrete tools for practical implementation for benefits at community level.BT/Environmental Biotechnolog

Got Whey? Sustainability Endpoints for the Dairy Industry through Resource Biorecovery

Whey has applications in food, beverages, personal care products, pharmaceuticals, and the medical sector. However, it remains a massive dairy residue worldwide (160.7 million m3 year−1), with high organic and nutrient loads. About 42% is used for low-value products such as animal feed and fertilizers or is even directly discharged into water streams, leading to ecosystem damage via eutrophication. We reviewed the uses and applications of cheese whey, along with associated environmental impacts and innovative ways to mitigate them using affordable and scalable technologies. Recycling and repurposing whey remain challenges for remote locations and poor communities with limited access to expensive technology. We propose a closed-loop biorefinery strategy to simultaneously mitigate environmental impacts and valorize whey resources. Anaerobic digestion utilizes whey to produce biogas and/or carboxylates. Alternative processes combining anaerobic digestion and low-cost open photobioprocesses can valorize whey and capture organic, nitrogenous, and phosphorous nutrients into microalgal biomass that can be used as food and crop supply or processed into biofuels, pigments, and antioxidants, among other value-added products. The complete valorization of cheese whey also depends on facilitating access to relevant information on whey production, identifying stakeholders, reducing technology gaps among countries, enforcing legislation and compliance, and creating subsidies and fostering partnerships with industries and between countries.BT/Environmental Biotechnolog

Got Whey? The significance of cheese whey at the confluence of dairying, environmental impacts, energy and resource biorecovery

Milk discovery and processing enabled human settling and thriving in various settings. The discovery of cheese led to the production of whey as dairy by-product. Although it can find application in food, beverages, personal care products, pharmaceuticals and medical treatment, cheese whey is a massive dairying residue world-wide (154 Mm3·y-1) with high organic and nutrient loads. About 42% is used as low-value products as animal feed and fertilisers or even directly discharged in water streams, leading to ecosystem damage by eutrophication. Recycling and repurposing whey remains a challenge for remote locations and poor communities with limited access to expensive technology. Anaerobic digestion is proven and accessible for utilizing whey as substrate to produce biogas and/or carboxylates. Alternative processes combining anaerobic digestion and low-cost open photobioprocesses can foster the valorisation of cheese whey and capture of organics and nitrogen and phosphorus nutrients into a microalgal biomass that can be used as food and crop supply or processed into biofuels, pigments, antioxi-dants, among other value-added products. Awareness should be raised about the economic potential of cheese whey surplus by developing an action plan that (i) identifies stakeholders, (ii) sets goals and achieves solutions, (iii) decreases technology gaps among countries, (iv) enforces legislation and compliance, and (v) creates subsidies and foments partnerships with industries and other countries for the full valorisation of whey. We propose a closed-loop biorefinery implementation strategy to simultaneously mitigate environmental impacts and valorise whey resources.BT/Environmental Biotechnolog

Catch me if you can: capturing microbial community transformation by extracellular DNA using Hi-C sequencing

The transformation of environmental microorganisms by extracellular DNA is an overlooked mechanism of horizontal gene transfer and evolution. It initiates the acquisition of exogenous genes and propagates antimicrobial resistance alongside vertical and conjugative transfers. We combined mixed-culture biotechnology and Hi-C sequencing to elucidate the transformation of wastewater microorganisms with a synthetic plasmid encoding GFP and kanamycin resistance genes, in the mixed culture of chemostats exposed to kanamycin at concentrations representing wastewater, gut and polluted environments (0.01–2.5–50–100 mg L−1). We found that the phylogenetically distant Gram-negative Runella (102 Hi-C links), Bosea (35), Gemmobacter (33) and Zoogloea (24) spp., and Gram-positive Microbacterium sp. (90) were transformed by the foreign plasmid, under high antibiotic exposure (50 mg L−1). In addition, the antibiotic pressure shifted the origin of aminoglycoside resistance genes from genomic DNA to mobile genetic elements on plasmids accumulating in microorganisms. These results reveal the power of Hi-C sequencing to catch and surveil the transfer of xenogenetic elements inside microbiomes

Syntrophy between fermentative and purple phototrophic bacteria to treat and valorize carbohydrate-rich wastewaters

Fermentative chemoorganoheterotrophic bacteria (FCB) and purple photoorganoheterotrophic bacteria (PPB) are two interesting microbial guilds to process carbohydrate-rich wastewaters. Their metabolic interactions have been studied in pure cultures or co-cultures, but little is known about mixed cultures. We studied the effect of reactor regimes (batch/chemostat) and illumination modes (continuous infrared light, dark, or light/dark cycles) on glucose conversions and process ecology of the interactions between FCB and PPB in mixed cultures. In batch, FCB (&gt;80 % of sequencing read counts) outcompeted PPB, under any light conditions. In chemostat under continuous and alternating irradiance, three FCB populations were enriched (&gt;70 %), while Rhodobacteraceae (PPB) made 30 % of the community. Glucose fermentation products were linked to the dominant FCB. Continuous culturing helped maintaining FCB and PPB in syntrophy: PPB grew on glucose metabolites produced by FCB. Engineering the association between FCB and PPB in mixed-culture processes can help to treat and valorize carbohydrate-rich aqueous waste.</p

Enrichment and Aggregation of Purple Non-sulfur Bacteria in a Mixed-Culture Sequencing-Batch Photobioreactor for Biological Nutrient Removal From Wastewater

Mixed-culture biotechnologies are widely used to capture nutrients from wastewater. Purple non-sulfur bacteria (PNSB), a guild of anoxygenic photomixotrophic organisms, rise interest for their ability to directly assimilate nutrients in the biomass. One challenge targets the aggregation and accumulation of PNSB biomass to separate it from the treated water. Our aim was to enrich and produce a concentrated, fast-settling PNSB biomass with high nutrient removal capacity in a 1.5-L, stirred-tank, anaerobic sequencing-batch photobioreactor (SBR). PNSB were rapidly enriched after inoculation with activated sludge at 0.1 gVSS L–1 in a first batch of 24 h under continuous irradiance of infrared (IR) light (&gt;700 nm) at 375 W m–2, with Rhodobacter reaching 54% of amplicon sequencing read counts. SBR operations with decreasing hydraulic retention times (48 to 16 h, i.e., 1–3 cycles d–1) and increasing volumetric organic loading rates (0.2–1.3 kg COD d–1 m–3) stimulated biomass aggregation, settling, and accumulation in the system, reaching as high as 3.8 g VSS L–1. The sludge retention time (SRT) increased freely from 2.5 to 11 days. Acetate, ammonium, and orthophosphate were removed up to 96% at a rate of 1.1 kg COD d–1 m–3, 77% at 113 g N d–1 m–3, and 73% at 15 g P d–1 m–3, respectively, with COD:N:P assimilation ratio of 100:6.7:0.9 m/m/m. SBR regime shifts sequentially selected for Rhodobacter (90%) under shorter SRT and non-limiting concentration of acetate during reaction phases, for Rhodopseudomonas (70%) under longer SRT and acetate limitation during reaction, and Blastochloris (10%) under higher biomass concentrations, underlying competition for substrate and photons in the PNSB guild. With SBR operations we produced a fast-settling biomass, highly (&gt;90%) enriched in PNSB. A high nutrient removal was achieved by biomass assimilation, reaching the European nutrient discharge limits. We opened further insights on the microbial ecology of PNSB-based processes for water resource recovery.</p

Free-floating extracellular DNA: systematic profiling of mobile genetic elements and antibiotic resistance from wastewater

The free-floating extracellular DNA (exDNA) fraction of microbial ecosystems harbors antibiotic resistance genes (ARGs) and mobile genetic elements (MGEs). Natural transformation of these xenogenetic elements can generate microbial cells resistant to one or more antibiotics. Isolating and obtaining high yield exDNA is challenging due to its low concentration in wastewater environments. Profiling exDNA is crucial to unravel the ecology of free-floating ARGs and MGEs and their contribution to horizontal transfer. We developed a method using chromatography to isolate and enrich exDNA without causing cell lysis from complex wastewater matrices like influent (9 µg exDNA out of 1 L), activated sludge (5.6 µg), and treated effluent (4.3 µg). ARGs and MGEs were metagenomically profiled for both the exDNA and intracellular DNA (iDNA) of activated sludge, and quantified by qPCR in effluent water. qPCR revealed that ARGs and MGEs are more abundant in the iDNA fraction while still significant on exDNA (100-1000 gene copies mL−1) in effluent water. The metagenome highlighted that exDNA is mainly composed of MGEs (65%). According to their relatively low abundance in the resistome of exDNA, ARGs uptake by natural transformation is likely not the main transfer mechanism. Although ARGs are not highly abundant in exDNA, the prevalence of MGEs in the exDNA fraction can indirectly promote antibiotic resistance development. The combination of this method with functional metagenomics can help to elucidate the transfer and development of resistances in microbial communities. A systematic profiling of the different DNA fractions will foster microbial risk assessments across water systems, supporting water authorities to delineate measures to safeguard environmental and public health.BT/Environmental BiotechnologyPattern Recognition and Bioinformatic