Near-complete depolymerization of polyesters with nano-dispersed enzymes. DelRe Christopher,Jiang Yufeng,Kang Philjun,Kwon Junpyo,Hall Aaron,Jayapurna Ivan,Ruan Zhiyuan,Ma Le,Zolkin Kyle,Li Tim,Scown Corinne D,Ritchie Robert O,Russell Thomas P,Xu Ting Nature Successfully interfacing enzymes and biomachinery with polymers affords on-demand modification and/or programmable degradation during the manufacture, utilization and disposal of plastics, but requires controlled biocatalysis in solid matrices with macromolecular substrates. Embedding enzyme microparticles speeds up polyester degradation, but compromises host properties and unintentionally accelerates the formation of microplastics with partial polymer degradation. Here we show that by nanoscopically dispersing enzymes with deep active sites, semi-crystalline polyesters can be degraded primarily via chain-end-mediated processive depolymerization with programmable latency and material integrity, akin to polyadenylation-induced messenger RNA decay. It is also feasible to achieve processivity with enzymes that have surface-exposed active sites by engineering enzyme-protectant-polymer complexes. Poly(caprolactone) and poly(lactic acid) containing less than 2 weight per cent enzymes are depolymerized in days, with up to 98 per cent polymer-to-small-molecule conversion in standard soil composts and household tap water, completely eliminating current needs to separate and landfill their products in compost facilities. Furthermore, oxidases embedded in polyolefins retain their activities. However, hydrocarbon polymers do not closely associate with enzymes, as their polyester counterparts do, and the reactive radicals that are generated cannot chemically modify the macromolecular host. This study provides molecular guidance towards enzyme-polymer pairing and the selection of enzyme protectants to modulate substrate selectivity and optimize biocatalytic pathways. The results also highlight the need for in-depth research in solid-state enzymology, especially in multi-step enzymatic cascades, to tackle chemically dormant substrates without creating secondary environmental contamination and/or biosafety concerns. 10.1038/s41586-021-03408-3
    Mediterranean grassland soil C-N compound turnover is dependent on rainfall and depth, and is mediated by genomically divergent microorganisms. Diamond Spencer,Andeer Peter F,Li Zhou,Crits-Christoph Alexander,Burstein David,Anantharaman Karthik,Lane Katherine R,Thomas Brian C,Pan Chongle,Northen Trent R,Banfield Jillian F Nature microbiology Soil microbial activity drives the carbon and nitrogen cycles and is an important determinant of atmospheric trace gas turnover, yet most soils are dominated by microorganisms with unknown metabolic capacities. Even Acidobacteria, among the most abundant bacteria in soil, remain poorly characterized, and functions across groups such as Verrucomicrobia, Gemmatimonadetes, Chloroflexi and Rokubacteria are understudied. Here, we have resolved 60 metagenomic and 20 proteomic data sets from a Mediterranean grassland soil ecosystem and recovered 793 near-complete microbial genomes from 18 phyla, representing around one-third of all microorganisms detected. Importantly, this enabled extensive genomics-based metabolic predictions for these communities. Acidobacteria from multiple previously unstudied classes have genomes that encode large enzyme complements for complex carbohydrate degradation. Alternatively, most microorganisms encode carbohydrate esterases that strip readily accessible methyl and acetyl groups from polymers like pectin and xylan, forming methanol and acetate, the availability of which could explain the high prevalence of C metabolism and acetate utilization in genomes. Microorganism abundances among samples collected at three soil depths and under natural and amended rainfall regimes indicate statistically higher associations of inorganic nitrogen metabolism and carbon degradation in deep and shallow soils, respectively. This partitioning decreased in samples under extended spring rainfall, indicating that long-term climate alteration can affect both carbon and nitrogen cycling. Overall, by leveraging natural and experimental gradients with genome-resolved metabolic profiles, we link microorganisms lacking prior genomic characterization to specific roles in complex carbon, C, nitrate and ammonia transformations, and constrain factors that impact their distributions in soil. 10.1038/s41564-019-0449-y
    Lignocellulolytic systems of soil bacteria: A vast and diverse toolbox for biotechnological conversion processes. López-Mondéjar Rubén,Algora Camelia,Baldrian Petr Biotechnology advances Lignocellulose from plant biomass represents an abundant and renewable source for the production of environmentally friendly chemicals and biofuels. However, its recalcitrant nature entails the use of complex biochemical reactions that are still challenging. Since the degradation of lignocellulose is the current bottleneck of the conversion processes, the search for novel enzymes and microbial strains for degrading plant biomass is of high importance. Currently, bacteria are in the spotlight as promising candidates for novel conversion strategies due to their wide functional diversity and versatility. Here, we review the lines of evidence that show the high potential of bacterial strains from soil for biomass conversion ranging from strain characterization to metagenome and metatranscriptome analysis. Substantial and diverse fractions of soil bacteria are able to decompose the major lignocellulose components. To do that, bacteria evolved structurally variable and often highly complex lignocellulolytic systems composed of enzymes as well as proteins involved in efficient substrate binding. Both as individual components or in combination, bacterial enzymes, and accessory proteins appear to be promising tools in the biotechnological valorization of lignocellulose. 10.1016/j.biotechadv.2019.03.013
    Centimeter-Long Microbial Electron Transport for Bioremediation Applications. Yuan Yong,Zhou Lihua,Hou Rui,Wang Yi,Zhou Shungui Trends in biotechnology Microbial bioremediation based on nano- to micrometer-scale electron transport has been intensively studied during the past decade, but its application can be hindered by a deficiency of suitable electron acceptors or slow mass transportation at contaminated sites. Microbial long-distance electron transport (LDET), which can couple spatially separated redox reactions across distances in natural environments, has recently emerged at centimeter-length scales. LDET explains a range of globally important biogeochemical phenomena and overcomes the drawbacks of conventional bioremediation by directly linking distant electron donors and acceptors. Here, we highlight recent research outcomes in examining, characterizing, and engineering LDET, and describe how LDET can be exploited to develop advanced technologies for the bioremediation of soils and sediments. 10.1016/j.tibtech.2020.06.011
    Nanomaterials Facilitating Microbial Extracellular Electron Transfer at Interfaces. Wang Ruiwen,Li Huidong,Sun Jinzhi,Zhang Lu,Jiao Jia,Wang Qingqing,Liu Shaoqin Advanced materials (Deerfield Beach, Fla.) Electrochemically active bacteria can transport their metabolically generated electrons to anodes, or accept electrons from cathodes to synthesize high-value chemicals and fuels, via a process known as extracellular electron transfer (EET). Harnessing of this microbial EET process has led to the development of microbial bio-electrochemical systems (BESs), which can achieve the interconversion of electrical and chemical energy and enable electricity generation, hydrogen production, electrosynthesis, wastewater treatment, desalination, water and soil remediation, and sensing. Here, the focus is on the current understanding of the microbial EET process occurring at both the bacteria-electrode interface and the biotic interface, as well as some attempts to improve the EET by using various nanomaterials. The behavior of nanomaterials in different EET routes and their influence on the performance of BESs are described. The inherent mechanisms will guide rational design of EET-related materials and lead to a better understanding of EET mechanisms. 10.1002/adma.202004051
    Using Microbial Aggregates to Entrap Aqueous Phosphorus. Xu Ying,Wu Yonghong,Esquivel-Elizondo Sofia,Dolfing Jan,Rittmann Bruce E Trends in biotechnology The increasing use and associated loss of phosphorus to the environment pose risks to aquatic ecosystems. Technology for phosphorus removal based on microbial aggregates is a natural, ecologically widespread, and sustainable reclamation strategy. Two main processes dominate phosphorus removal by microbial aggregates: extra- and intra-cellular entrapment. Extracellular phosphorus entrapment relies on extracellular polymeric substances, while intracellular entrapment uses a wider variety of phosphorus-entrapping mechanisms. In microbial aggregates, microalgae-bacteria interactions, quorum sensing, and acclimation can enhance phosphorus removal. Based on these insights, we propose novel avenues for entrapping phosphorus using ecological and genetic engineering, manipulated interactions, and integrated processes to create phosphorus removal technology mediated by microbial aggregates. 10.1016/j.tibtech.2020.03.012
    Upgrading of marine (fish and crustaceans) biowaste for high added-value molecules and bio(nano)-materials. Maschmeyer Thomas,Luque Rafael,Selva Maurizio Chemical Society reviews Currently, the Earth is subjected to environmental pressure of unprecedented proportions in the history of mankind. The inexorable growth of the global population and the establishment of large urban areas with increasingly higher expectations regarding the quality of life are issues demanding radically new strategies aimed to change the current model, which is still mostly based on linear economy approaches and fossil resources towards innovative standards, where both energy and daily use products and materials should be of renewable origin and 'made to be made again'. These concepts have inspired the circular economy vision, which redefines growth through the continuous valorisation of waste generated by any production or activity in a virtuous cycle. This not only has a positive impact on the environment, but builds long-term resilience, generating business, new technologies, livelihoods and jobs. In this scenario, among the discards of anthropogenic activities, biodegradable waste represents one of the largest and highly heterogeneous portions, which includes garden and park waste, food processing and kitchen waste from households, restaurants, caterers and retail premises, and food plants, domestic and sewage waste, manure, food waste, and residues from forestry, agriculture and fisheries. Thus, this review specifically aims to survey the processes and technologies for the recovery of fish waste and its sustainable conversion to high added-value molecules and bio(nano)materials. 10.1039/c9cs00653b
    Engineering microbial peer pressure. Johnston Chad W,Collins James J Science (New York, N.Y.) 10.1126/science.aay3157