Down in the pond: Isolation and characterization of a new Serratia marcescens strain (LVF3) from the surface water near frog’s lettuce (Groenlandia densa)

Serratia marcescens is a species that belongs to the family of Yersiniaceae. This family comprises taxa representing opportunistic human- and phytopathogens but also plant growth-promoting rhizobacteria (PGPR). This study describes a novel Gram-negative strain (LVF3R) of the species Serratia marcescens. The strain was characterized genomically, morphologically, and physiologically. In addition, the potential of the isolate to act as a host strain to assess the diversity of Serratia associated phages in environmental samples was explored. Average nucleotide identity analysis revealed that LVF3R belongs to the species Serratia marcescens. In silico analysis and ProphageSeq data resulted in the identification of one prophage, which is capable of viral particle formation. Electron microscopy showed cells of a rod-shaped, flagellated morphotype. The cells revealed a length and width of 1–1.6 μm and 0.8 μm, respectively. LVF3R showed optimal growth at 30 C and in the presence of up to 2% (w/v) NaCl. It exhibited resistances to ampicillin, erythromycin, oxacillin, oxytetracycline, rifampicin, tetracycline, and vancomycin. Genome data indicate that strain S. marcescens LVF3R is a potential PGPR strain. It harbors genes coding for indole acetic acid (IAA) biosynthesis, siderophore production, plant polymer degradation enzymes, acetoin synthesis, flagellar proteins, type IV secretion system, chemotaxis, phosphorous solubilization, and biofilm formation.

Aromatic dimer dehydrogenases from Novosphingobium aromaticivorans reduce monoaromatic diketones

Lignin is a potential source of valuable chemicals, but its chemical depolymerization results in a heterogeneous mixture of aromatics and other products. Microbes could valorize depolymerized lignin by converting multiple substrates into one or a small number of products. In this study, we describe the ability of Novosphingobium aromaticivorans to metabolize 1-(4-hydroxy-3-methoxyphenyl)propane-1,2-dione (G-diketone), an aromatic Hibbert diketone which is produced during formic acid-catalyzed lignin depolymerization. By assaying genome-wide transcript levels from N. aromaticivorans during growth on G-diketone and other chemically-related aromatics, we hypothesized that the Lig dehydrogenases, previously characterized as oxidizing β-O-4 linkages in aromatic dimers, were involved in G-diketone metabolism by N. aromaticivorans . Using purified N. aromaticivorans Lig dehydrogenases, we found that LigL, LigN, and LigD each reduced the Cα ketone of G-diketone in vitro but with different substrate specificities and rates. Furthermore, LigL, but not LigN or LigD, also reduced the Cα ketone of 2-hydroxy-1-(4-hydroxy-3-methoxyphenyl)propan-1-one (GP-1) in vitro , a derivative of G-diketone with the Cβ ketone reduced, when GP-1 was provided as a substrate. The newly identified activity of these Lig dehydrogenases expands the potential range of substrates utilized by N. aromaticivorans beyond what has been previously recognized. This is beneficial both for metabolizing a wide range of natural and non-native depolymerized lignin substrates and for engineering microbes and enzymes that are active with a broader range of aromatic compounds. Importance Lignin is a major plant polymer composed of aromatic units that have value as chemicals. However, the structure and composition of lignin has made it difficult to use this polymer as a renewable source of industrial chemicals. Bacteria like Novosphingobium aromaticivorans have the potential to make chemicals from lignin not only because of their natural ability to metabolize a variety of aromatics but also because there are established protocols to engineer N. aromaticivorans strains to funnel lignin-derived aromatics into valuable products. In this work, we report a newly discovered activity of previously characterized dehydrogenase enzymes with a chemically-modified byproduct of lignin depolymerization. We propose that the activity of N. aromaticivorans enzymes with both native lignin aromatics and those produced by chemical depolymerization will expand opportunities for producing industrial chemicals from the heterogenous components of this abundant plant polymer.

From roots to leaves: the capacity of Micromonospora to colonize different legume tissues

An important number of Micromonospora strains have been reported from nitrogen fixing root nodules of legume and actinorhizal plants. However, the question of whether this bacterium can also be found in other parts of these plants remains unanswered. Over 150 strains were recovered from different Lupinus angustifolius and Pisum sativum tissues including leaves, stems, roots, and nodules. Ninety-seven percent of the isolates were identified by 16S rRNA gene sequence in the target genus and were associated with 27 different Micromonospora species. Plant-polymer degrading enzymes are suspected to play a role in the colonization of plants. To this end, bacterial enzymatic activity assays for amylases, cellulases, chitinases, pectinases and xylanases were determined. All strains produced xylanases and pectinases, while 98.6%, 98%, and 94.6% of them produced amylases, cellulases, and chitinases, respectively. The most productive strains included seven isolates from P. sativum and one from L. angustifolius. Strain Micromonospora lupini ML01-gfp was used to determine its capacity to reach and colonize different plant organs using P. sativum as the plant model. Stem and leaf samples were monitored by optical and fluorescence microscopy to locate the tagged strain. These results strongly suggest that Micromonospora is able, not only to infect nitrogen-fixing nodules, but also of reaching other parts of the host plant, especially the leaves.

The activity and functions of subarctic soil microbial communities vary across vegetation types

Global warming changes the activity of soil microbial communities in high latitudes, which might result in higher greenhouse gas emissions. However, these microbial processes involved in GHG production and consumption are not thoroughly understood. We analyzed 116 soil metatranscriptomes from 73 tundra sites and investigated how bacterial and archaeal communities and their functions vary horizontally (i.e. vegetation type) and vertically (i.e. topsoil organic and mineral layers) during the summer season, in soil types that differed in pH, moisture, soil organic matter (SOM), carbon and nitrogen content. Active microbial communities were significantly different in the organic and mineral soil layers. Additionally, the communities differed significantly between the different vegetation types both in the organic and mineral layers. Various plant polymer degraders were particularly active in shrub-dominated ecosystems with high SOM and low pH, whereas less known mixotrophic groups such as Chloroflexi were active in graminoid-dominated soil with lower SOM and higher pH. Additionally, we detected transcripts of alphaproteobacterial methanothrophs, which potentially moderate methane release from tundra soils in deeper soil layer. Our results provide new insights into the diversity and activity of microbial communities of the high-latitudes under climate change.

Deconstruction of Lignin: From Enzymes to Microorganisms

Lignocellulosic residues are low-cost abundant feedstocks that can be used for industrial applications. However, their recalcitrance currently makes lignocellulose use limited. In natural environments, microbial communities can completely deconstruct lignocellulose by synergistic action of a set of enzymes and proteins. Microbial degradation of lignin by fungi, important lignin degraders in nature, has been intensively studied. More recently, bacteria have also been described as able to break down lignin, and to have a central role in recycling this plant polymer. Nevertheless, bacterial deconstruction of lignin has not been fully elucidated yet. Direct analysis of environmental samples using metagenomics, metatranscriptomics, and metaproteomics approaches is a powerful strategy to describe/discover enzymes, metabolic pathways, and microorganisms involved in lignin breakdown. Indeed, the use of these complementary techniques leads to a better understanding of the composition, function, and dynamics of microbial communities involved in lignin deconstruction. We focus on omics approaches and their contribution to the discovery of new enzymes and reactions that impact the development of lignin-based bioprocesses.

Economic and mathematical approach to optimization of vacuum-freeze drying of the enzyme preparation inulinase Bacillus polymyxa 29

One of the promising directions of improving the processes of processing plant raw materials is bioconversion using enzyme preparations, the use of which allows you to significantly change, intensify and improve existing technologies for the production of food products as a system of energy-efficient processes. The subject of the study is the enzyme preparation of inulinase Bacillus polymyxa 29, which ensures the conversion of the plant polymer inulin to fructose. Fructose has an increased interest in food technologies as a safer human health alternative to sucrose. Fructose yield reaches 90–95%; the sweetness coefficient of fructose is 1.73 times higher than sucrose. Production of enzyme with maximum activity is achieved by vacuum-sublimation drying at time-programmed mode of heat supply control taking into account limitations due to quality of heat exchange and economic feasibility of the process. Method of selection of optimal solutions in vacuum-sublimation drying of feather preparation Bacillus polymyxa 29 according to profit index is proposed. The proposed approach resolved the main technical gap between productivity and energy consumption. An optimal loading of the sublimator has been established, which ensures the minimization of specific electric power consumption for various values of the initial moisture drying of the enzyme, taking into account the given efficiency of the vacuum sublimation dryer.

Functional and chemical characterization of XAF: a heat-stable plant polymer that activates xyloglucan endotransglucosylase/hydrolase (XTH)

Background and Aims Xyloglucan endotransglucosylase/hydrolase (XTH) proteins that possess xyloglucan endotransglucosylase (XET) activity contribute to cell-wall assembly and remodelling, orchestrating plant growth and development. Little is known about in-vivo XET regulation, other than at the XTH transcriptional level. Plants contain ‘cold-water-extractable, heat-stable polymers’ (CHPs) which are XTH-activating factors (XAFs) that desorb and thereby activate wall-bound XTHs. Because XAFs may control cell-wall modification in vivo, we have further explored their nature. Methods Material was cold-water-extracted from 25 plant species; proteins were precipitated by heat-denaturation, then CHP was ethanol-precipitated. For XAF assays, CHP (or sub-fractions thereof) was applied to washed Arabidopsis thaliana cell walls, and the enzymes thus solubilized were assayed radiochemically for XET activity. In some experiments, the CHP was pre-treated with trifluoroacetic acid (TFA), alkali (NaOH) or glycanases. Key Results CHP specifically desorbed wall-bound XTHs, but not β-glucosidases, phosphatases or peroxidases. CHP preparations from 25 angiosperms all possessed XAF activity but had no consistent monosaccharide composition. Of 11 individual plant polymers tested, only gum arabic and tamarind xyloglucan were XAF-active, albeit less so than CHP. On gel-permeation chromatography, XAF-active cauliflower CHP eluted with a molecular weight of ~7000–140 000, although no specific sugar residue(s) co-eluted exactly with XAF activity. Cauliflower XAF activity survived cold alkali and warm dilute TFA (which break ester and glycofuranosyl linkages, respectively), but was inactivated by hot 2 m TFA (which breaks glycopyranosyl linkages). Cauliflower XAF activity was remarkably stable to diverse glycanases and glycosidases. Conclusions XAFs are naturally occurring heat-stable polymers that specifically desorb (thereby activating) wall-bound XTHs. Their XAF activity considerably exceeds that of gum arabic and tamarind xyloglucan, and they were not identifiable as any major plant polysaccharide. We propose that XAF is a specific, minor, plant polymer that regulates xyloglucan transglycosylation in vivo, and thus wall assembly and restructuring.