A role of xylanase,alpha-L-arabinofuranosidase,and xylosidase in xylan degradation

Renewable natural resources such as xylans are abundant in many agricultural wastes. Penicillium sp. AHT-1 is a strong producer of xylanolytic enzymes. The sequential activities of its xylanase, alpha-L-arabinofuranosidase, and beta-xylosidase on model hemicellulose oat-spelt xylan was investigated. Optimum production of the enzymes was found in culture containing oat-spelt xylan at 30 degrees C and initial pH 7.0 after 6 days. The enzymes were partially purified by ammonium sulphate fractionation and anion-exchange chromatography on DEAE-Toyopearl 650 S. The apparent molecular mass was 21 kDa, and the protein displayed an "endo" mode of action. The xylanase exhibited glycotansferase activity. It synthesized higher oligosaccharides from the initial substrates, and xylotriose was the shortest unit of substrate transglycosylated. Xylanolytic enzymes (enzyme mixture) produced by this Penicillium sp. interacted cooperatively and sequentially in the hydrolysis of oat-spelt xylan in the following order: alpha-L-arabinofuranosidase --> xylanase --> beta-xylosidase. All three enzymes exhibited optimal activity under the same conditions (temperature, pH, cultivation), indicating that they alone are sufficient to completely depolymerize the test xylan. Results indicate that the xylanolytic enzyme mixture of Penicillium sp. AHT-1 could be useful for bioconversion of xylan-rich plant wastes to value-added products.     

Xylanase and acetyl xylan esterase activities of XynA,a key subunit of the Clostridium cellulovorans cellulosome for xylan degradation

The Clostridium cellulovorans xynA gene encodes the cellulosomal endo-1,4-beta-xylanase XynA, which consists of a family 11 glycoside hydrolase catalytic domain (CD), a dockerin domain, and a NodB domain. The recombinant acetyl xylan esterase (rNodB) encoded by the NodB domain exhibited broad substrate specificity and released acetate not only from acetylated xylan but also from other acetylated substrates. rNodB acted synergistically with the xylanase CD of XynA for hydrolysis of acetylated xylan. Immunological analyses revealed that XynA corresponds to a major xylanase in the cellulosomal fraction. These results indicate that XynA is a key enzymatic subunit for xylan degradation in C. cellulovorans.     

Utilization of cellulose,starch, xylan,and other hemicelluloses for growth by the rumen phycomyceteNeocallimastix frontalis

The rumen phycomyceteNeocallimastix frontalis was found to utilize for growth a wide range of plant polysaccharides, including cellulose, starch, and xylan. The ability to utilize polysaccharides was absent after prolonged culture in vitro on glucose, but present after subculture on grass particles. Grass-grown organisms were capable of growing at the expense of cellobiose, maltose, and xylose, capacities absent before exposure to grass particles.N. frontalis cultures digested at least 41% of the dry weight of water-insoluble grass tissue, and up to 75% of the dry weight of filter paper.     

Recognition and degradation of chitin by streptomycetes

Chitin is the second most abundant renewable polysaccharide, as it is a component of the exoskeleton of many organisms and of the cell walls of numerous fungi. Most streptomycetes secrete a number of chitinases, hydrolyzing chitin to oligomers, chitobiose or N-acetylglucosamine which can be utilized as carbon or nitrogen source. The chitinases of several streptomycetes have been shown to have a modular arrangement comprising catalytic, substrate binding as well as linker domains. Moreover, during growth in the presence of chitin-containing substrates, many Streptomycesstrains have been shown to secrete formerly unknown, small (about 200 aa) chitin binding proteins (CHBs) which lack enzymatic activity and specifically target and invade chitin. Several motifs, including the relative location and spacing of four tryptophan residues, are conserved in the investigated CHB types, CHB1 and CHB2. The affinity of CHB1 to crab shell chitin is two times higher than that of CHB2. Comparative studies of various generated mutant CHB1 proteins led to the conclusion that it is one of the exposed tryptophan residues that directly contributes to the interaction with chitin. On the basis of immunological, biochemical and physiological studies, it can be concluded that the CHBs act like a glue with which streptomycetes target chitin-containing samples or organisms. The ecological implications of these findings are discussed.     

Physiology of microbial degradation of chitin and chitosan

Chitin is produced in enormous quantities in the biosphere, chiefly as the major structural component of most fungi and invertebrates. Its degradation is chiefly by bacteria and fungi, by chitinolysis via chitinases, but also via deacetylation to chitosan, which is hydrolysed by chitosanases. Chitinases and chitosanases have a range of roles in the organisms producing them: autolytic, morphogenetic or nutritional. There are increasing examples of their roles in pathogenesis and symbiosis. A range of chitinase genes have been cloned, and the potential use for genetically manipulated organisms over-producing chitinases is being investigated. Chitinases also have a range of uses in processing chitinous material and producing defined oligosaccharides.     

Application of cellulase and hemicellulase to pure xylan, pure cellulose, and switchgrass solids from leading pretreatments

Accellerase 1000 cellulase, Spezyme CP cellulase, β-glucosidase, Multifect xylanase, and beta-xylosidase were evaluated for hydrolysis of pure cellulose, pure xylan, and switchgrass solids from leading pretreatments of dilute sulfuric acid, sulfur dioxide, liquid hot water, lime, soaking in aqueous ammonia, and ammonia fiber expansion. Distinctive sugar release patterns were observed from Avicel, phosphoric acid swollen cellulose (PASC), xylan, and pretreated switchgrass solids, with accumulation of significant amounts of xylooligomers during xylan hydrolysis. The strong inhibition of cellulose hydrolysis by xylooligomers could be partially attributed to the negative impact of xylooligomers on cellulase adsorption. The digestibility of pretreated switchgrass varied with pretreatment but could not be consistently correlated to xylan, lignin, or acetyl removal. Initial hydrolysis rates did correlate well with cellulase adsorption capacities for all pretreatments except lime, but more investigation is needed to relate this behavior to physical and compositional properties of pretreated switchgrass.     

Effect of humic acid on anaerobic digestion of cellulose and xylan in completely stirred tank reactors: inhibitory effect,mitigation of the inhibition and the dynamics of the microbial communities.

Applied Microbiology and Biotechnology - Inhibition effect of humic acid (HA) on anaerobic digestion of cellulose and xylan and the mitigation potential of the inhibition were evaluated in...     

Characterization of marine prokaryotic communities via DNA and RNA

We know very little about species distributions in prokaryotic marine plankton. Such information is very interesting in its own right, and ignorance of it is also beginning to hamper process studies, such as those on viral infection. New DNA- and RNA-based approaches avoid many prior limitations. Here we discuss four such applications: (1) cloning and sequencing of 16S rRNA genes to produce lists of what types of organisms are present; (2) quantification of these individual types in marine samples by nucleic acid hybridization, including single cell fluorescence; (3) quantitative comparison by DNA-DNA hybridization of entire microbial communities in terms of shared common types, without knowledge of community components; and (4) finding cultures that are representative of native communities. Several previously uncharacterized types of bacteria and archaea (probably including novel phyla) are present in marine plankton. Evidence from both the Atlantic and Pacific suggests that as-of-yet uncultivated archaea may dominate the deep sea, and thus may be the most abundant group of organisms on Earth. Such archaea are in surface waters as well, and can be visualized with fluorescent probes and enriched at room temperature with addition of organic nutrients. Community hybridization shows that variability of microbial community compositions in time and space is high. Although most native bacteria do not grow in culture, some proteobacterial cultures appear by genomic hybridization to be representative of certain communities. These and other results indicate the utility of DNA- and RNA-based methods.     

Effects of xylan and starch on secretome of the basidiomycete Phanerochaete chrysosporium grown on cellulose

Lignocellulosic biomass contains cellulose and xylan as major structural components, and starch as a storage polysaccharide. In the present study, we have used comparative secretomic analysis to examine the effects of xylan and starch on the expression level of proteins secreted by the basidiomycete Phanerochaete chrysosporium grown on cellulose,. Forty-seven spots of extracellular proteins expressed by P. chrysosporium separated by two-dimensional electrophoresis were identified by liquid chromatography-tandem mass spectrometry analysis. Addition of starch to the cellulolytic culture did not affect fungal growth significantly, but did decrease the production of total extracellular enzymes, including cellulases and xylanases. In contrast, addition of xylan increased mycelial volume and the production of extracellular proteins. Xylan increased synthesis of several glycoside hydrolase (GH) family 10 putative endoxylanases and a putative glucuronoyl esterase belonging to carbohydrate esterase family 15, for which plant cell wall xylan may be a substrate. Moreover, cellobiose dehydrogenase and GH family 61 proteins, which are known to promote cellulose degradation, were also increased in the presence of xylan. These enzymes may contribute to degradation by the fungus of not only cellulose but also complex carbohydrate components of the plant cell wall.     

Soil microbial communities drive the resistance of ecosystem multifunctionality to global change in drylands across the globe

The relationship between soil microbial communities and the resistance of multiple ecosystem functions linked to C, N and P cycling (multifunctionality resistance) to global change has never been assessed globally in natural ecosystems. We collected soils from 59 dryland ecosystems worldwide to investigate the importance of microbial communities as predictor of multifunctionality resistance to climate change and nitrogen fertilisation. Multifunctionality had a lower resistance to wetting–drying cycles than to warming or N deposition. Multifunctionality resistance was regulated by changes in microbial composition (relative abundance of phylotypes) but not by richness, total abundance of fungi and bacteria or the fungal: bacterial ratio. Our results suggest that positive effects of particular microbial taxa on multifunctionality resistance could potentially be controlled by altering soil pH. Together, our work demonstrates strong links between microbial community composition and multifunctionality resistance in dryland soils from six continents, and provides insights into the importance of microbial community composition for buffering effects of global change in drylands worldwide.     

In vivo degradation of oxidized, regenerated cellulose

Oxidized, regenerated cellulose (ORC) was surgically implanted on the uterine horns of rabbits, and its biodegradation was studied in vivo. Samples of peritoneal lavages, serum, and urine were collected during the degradation process and analyzed for carbohydrate components utilizing high-performance liquid chromatography with pulsed amperometric detection (h.p.l.c.-p.a.d.). Degradation was rapid, and oligomeric products were evident primarily in the peritoneal fluid from the implantation site, with no apparent accumulation in either the serum or the urine. The size distribution and the amount of the oligomeric products decreased after day one, and by day four peritoneal lavages were essentially free of oligomers. The structure of the products formed was consistent with the lability of the polymer in solution, and the kinetics of degradation paralleled the results of the previously reported in vitro studies. Rabbit peritoneal macrophages, when incubated with ORC in vitro were observed to readily ingest and hydrolyze the polymeric material. A mechanism of degradation consisting of chemical depolymerization, followed by enzymatic hydrolysis mediated by glycosidases endogenous to peritoneal macrophages, is proposed.     

Diversity of aquatic prokaryotic communities in the Cuatro Cienegas basin

The Cuatro Cienegas basin (Coahuila, México) is a composite of different water systems in the middle of the desert with unusually high levels of endemism and diversity in different taxa. Although the diversity of macrobiota has been well described, little is known about the diversity and distribution of microorganisms in the oligotrophic ponds. Here we describe the extent and distribution of diversity found in aquatic prokaryotic communities by analysis of terminal restriction fragment length polymorphisms (T-RFLP) of 16S rRNA genes and phylogenetic analysis of cloned genes. Twelve locations within the basin were sampled. Among all the samples, we found a total of 117 operational taxonomic units (OTUs) using T-RFLPs, which ranged in any single sample from four to 49. OTU richness and Shannon diversity indices for different sites varied, but none were particularly high. 16S rRNA gene sequence data showed 68 different phylotypes among 198 clones. The most abundant phylotypes were Gamma- and Betaproteobacteria, and extreme halophiles. The differences among sites were significant; 45 TRFs were found only once, and 37% of the total diversity was represented by differences between sites, suggesting high beta-diversity. Further studies are needed to test whether this is a direct consequence of environmental heterogeneity in the basin.     

Multifunctional coating films by layer-by-layer deposition of cellulose and chitin nanofibrils

An environmentally benign surface modification process for plastic films was demonstrated by fabricating composite coatings through layer-by-layer assembly with green solid materials: aqueous dispersions of two kinds of crystalline polysaccharide nanofibrils. Anionic cellulose nanofibrils were obtained by the TEMPO (2,2,6,6-tetramethylpiperidine-1-oxyl radical)-mediated oxidation of native cellulose, while cationic β-chitin nanofibrils were prepared by the protonation of squid pen chitin. Uniform layer depositions, driven by electrostatic attraction and enhanced by hydrogen bonding, were observed on silicon wafers and then reproduced onto poly(ethylene terephthalate) films. Contact angle measurements and dyeing tests on the resulting films revealed their hydrophilic nature and the sorption of both charged and uncharged substances. Antireflection properties were also confirmed via the light transmittance measurements. As might be presumed from all these properties, this composite coating exhibited its unique behavior largely due to its structure, which was distinct from both those of nanofibril cast films and polymer films.     

Diversity and productivity of plant communities across the Inland Northwest,USA

No definitive explanation for the form of the relationship between species diversity and ecosystem productivity exists nor is there agreement on the mechanisms linking diversity and productivity across scales. Here, we examine changes in the form of the diversity–productivity relationship within and across the plant communities at three observational scales: plots, alliances, and physiognomic vegetation types (PVTs). Vascular plant richness data are from 4,760 20 m² vegetation field plots. Productivity estimates in grams carbon per square meter are from annual net primary productivity (ANPP) models. Analyses with generalized linear models confirm scale dependence in the species diversity–productivity relationship. At the plot focus, the observed diversity–productivity relationship was weak. When plot data were aggregated to a focus of vegetation alliances, a hump-shaped relationship was observed. Species turnover among plots cannot explain the observed hump-shaped relationship at the alliance focus because we used mean plot richness across plots as our index of species richness for alliances and PVTs. The sorting of alliances along the productivity gradient appears to follow regional patterns of moisture availability, with alliances that occupy dry environments occurring within the increasing phase of the hump-shaped pattern, alliances that occupy mesic to hydric environments occurring near the top or in the decreasing phase of the curve, and alliances that occupy the wettest environments having the fewest species and the highest ANPP. This pattern is consistent with the intermediate productivity theory but appears to be inconsistent with the predictions of water–energy theory.     

Influence of lignin and its degradation products on enzymatic hydrolysis of xylan

The influence of lignin, lignin model compounds, and black liquor from the kraft pulping process on the hydrolysis of xylan by xylanase was investigated. Addition of vanillic acid, acetovanillone, and protocatechuic acid increased the rate of hydrolysis of xylan by as much as 18–50% at low concentrations, but reached maxima at about 0.05% concentration. Addition of vanillin caused a 15% improvement in xylan hydrolysis, while addition of guaiacol more than doubled the hydrolysis rate. Increasing concentrations of either lignin or black liquor also increased the hydrolysis rate of xylan. Circular dichroism spectroscopy indicated a change in the structure of xylanase in the presence of black liquor.     

Historical and contemporary processes drive global phylogenetic structure across geographical scales: Insights from bat communities

Aim

Patterns of evolutionary relatedness among co-occurring species are driven by scale-dependent contemporary and historical processes. Yet, we still lack a detailed understanding of how these drivers impact the phylogenetic structure of biological communities. Here, we focused on bats (one of the most species-rich and vagile groups of mammals) and tested the predictions of three general biogeographical hypotheses that are particularly relevant to understanding how palaeoclimatic stability, local diversification rates and geographical scales shaped their present-day phylogenetic community structure.

Location

World-wide, across restrictive geographical extents: global, east–west hemispheres, biogeographical realms, tectonic plates, biomes and ecoregions.

Time period

Last Glacial Maximum (~22,000 years ago) to the present.

Major taxa studied

Bats (Chiroptera).

Methods

We estimated bat phylogenetic community structure across restrictive geographical extents and modelled it as a function of palaeoclimatic stability and in situ net diversification rates.

Results

Limiting geographical extents from larger to smaller scales greatly changed the phylogenetic structure of bat communities. The magnitude of these effects is less noticeable in the western hemisphere, where frequent among-realm biota interchange could have been maintained through the adaptive traits of bats. Bat communities with high phylogenetic relatedness are generally more common in regions that have changed less in climate since the Last Glacial Maximum, supporting the expectation that stable climates allow for increased phylogenetic clustering. Finally, increased in situ net diversification rates are associated with greater phylogenetic clustering in bat communities.

Main conclusions

We show that the world-wide phylogenetic structure of bat assemblages varies as a function of geographical extents, dispersal barriers, palaeoclimatic stability and in situ diversification. The integrative framework used in our study, which can be applied to other taxonomic groups, has not only proved useful to explain the evolutionary dynamics of community assembly, but could also help to tackle questions related to scale dependence in community ecology and biogeography.