Joining the forces of reactor microbiomes and electrochemistry: production of drop-in fuels from complex biomass and electrical energy.

Single cell techniques like flow cytometry combined with viability staining can help to obtain information on viability states of bacteria. Many fluorescent dyes are available for this purpose and can be chosen according to the available excitation source, the species used, and the background of scientific questions and relevant specifications. Within this short overview, we focus on two diverse groups of bacteria: the gram2 Escherichia coli and representatives of the gram+ Mycobacterium to demonstrate differences and similarities in dye uptake principles, processing and binding. We call for attention to possible diverse responses of different species to various viability assays. The cell surface structure of bacteria and the chemical properties of fluorescent probes considerably determine the success of a certain staining practice. Particular focus was drawn on analysis of membrane integrity, uptake of substrates and transformation of fluorogenic substrates. '

Background: Biogas production from lignocellulosic feedstock not competing with food production can contribute to a sustainable bioenergy system. The hydrolysis is the rate-limiting step in the anaerobic digestion of solid substrates such as straw. Hence, a detailed understanding of the metabolic processes during the steps of hydrolysis and acidogenesis is required to improve process control strategies.

Medium-chain carboxylates such as n-caproate and n-caprylate are valuable chemicals, which can be produced from renewable feedstock by anaerobic fermentation and lactate-based microbial chain elongation. Acidogenic microbiota involved in lactatebased chain elongation and their interplay with lactic acid bacteria have not been characterized in detail yet. Here, the metabolic and community dynamics were studied in a continuous bioreactor with xylan and lactate as sole carbon sources. Four succession stages were observed during 148 days of operation. After an adaptation period of 36 days, a relatively stable period of 28 days (stage I) was reached with n-butyrate, ncaproate and n-caprylate productivities of 7.2, 8.2 and 1.8 gCOD L −1 d −1 , respectively. After a transition period, the process changed to another period (stage II), during which 46% more n-butyrate, 51% less n-caproate and 67% less n-caprylate were produced. Co-occurrence networks of species based on 16S rRNA amplicon sequences and correlations with process parameters were analyzed to infer ecological interactions and potential metabolic functions. Diverse functions including hydrolysis of xylan, primary fermentation of xylose to acids (e.g., to acetate by Syntrophococcus, to n-butyrate by Lachnospiraceae, and to lactate by Lactobacillus) and chain-elongation with lactate (by Ruminiclostridium 5 and Pseudoramibacter) were inferred from the metabolic network. In stage I, the sub-network characterized by strongest positive correlations was mainly related to the production of n-caproate and n-caprylate. Lactic acid bacteria of the genus Olsenella co-occurred with potentially chain-elongating bacteria of the genus Pseudoramibacter, and their abundance was positively correlated with n-caproate and n-caprylate concentrations. A new sub-network appeared in stage II, which was mainly related to n-butyrate production and revealed a network of different lactic acid bacteria (Bifidobacterium) and potential n-butyrate producers (Clostridium sensu stricto 12). The synergy effects between lactate-producing and lactate-consuming bacteria constitute a division of labor cooperation of mutual benefit. Besides cooperation, competition between different taxa determined the bacterial community assembly over