Bacteria and lignin degradation

Lignin is both the most abundant aromatic (phenolic) polymer and the second most abundant raw material. It is degraded and modified by bacteria in the natural world, and bacteria seem to play a leading role in decomposing lignin in aquatic ecosystems. Lignin-degrading bacteria approach the polymer by mechanisms such as tunneling, erosion, and cavitation. With the advantages of immense environmental adaptability and biochemical versatility, bacteria deserve to be studied for their ligninolytic potential.     

白蚁消化系统转化和降解木质纤维素酶研究进展

木质纤维素是地球上最丰富的有机聚合物,白蚁是古老但进化最成功的高效木质纤维素降解者之一。了解白蚁降解高度抗性植物聚合物的机制对工业上生物质能源转化和生物仿生设计有重要的借鉴和指导价值。白蚁和其共生微生物产生的木质纤维素酶在其转化利用木质纤维素上发挥着重要作用。本文从来源作用方面对白蚁自身及其肠道原虫、细菌和真菌产生的纤维素酶、木聚糖酶和漆酶等酶研究概况进行了总结,对其存在的问题和前景进行了展望。本综述有助于全面了解白蚁消化系统木质纤维素酶的基因种类、来源、分布、表达以及酶活性和功能。     

海洋微生物产纤维素酶及其应用研究进展

纤维素是地球上最古老、最丰富的天然高分子,是天然可再生资源。纤维素酶广泛存在于自然界的生物体中,细菌、真菌和动物体内都能产生纤维素酶。微生物产纤维素酶已有较多报道,并在食品、医药、饲料、洗涤、纺织和造纸工业等领域有广阔的应用前景。海洋是一个巨大的资源库,海洋微生物产纤维素酶已经受到了广泛的关注。对产纤维素酶海洋微生物的种群、来源及基因筛选、海洋微生物产纤维素酶的酶学特性,以及纤维素酶的应用领域等方面的研究进展进行了简要综述,并对海洋微生物产纤维素酶的研究进行了展望。     

Lignin degradation by microorganisms: A review

Lignin is an abundant plant-based biopolymer that has found applications in a variety of industries from construction to bioethanol production. This recalcitrant branched polymer is naturally degraded by many different species of microorganisms, including fungi and bacteria. These microbial lignin degradation mechanisms provide a host of possibilities to overcome the challenges of using harmful chemicals to degrade lignin biowaste in many industries. The classes and mechanisms of different microbial lignin degradation options available in nature form the primary focus of the present review. This review first discusses the chemical building blocks of lignin and the industrial sources and applications of this multifaceted polymer. The review further places emphasis on the degradation of lignin by natural means, discussing in detail the lignin degradation activities of various fungal and bacterial species. The lignin-degrading enzymes produced by various microbial species, specifically white-rot fungi, brown-rot fungi, and bacteria, are described. In the end, possible directions for future lignin biodegradation applications and research investigations have been provided.     

Physiological aspects of chitin catabolism in marine bacteria

Chitin, a carbohydrate polymer composed of alternating beta-1, 4-linked N-acetylglucosamine residues is the second most abundant organic compound in nature. In the aquatic biosphere alone, it is estimated that more than 10(11) metric tons of chitin are produced annually. If this enormous quantity of insoluble carbon and nitrogen was not converted to biologically useful material, the oceans would be depleted of these elements in a matter of decades. In fact, marine sediments contain only traces of chitin, and the turnover of the polysaccharide is attributed primarily to marine bacteria, but the overall process involves many steps, most of which remain to be elucidated. Marine bacteria possess complex signal transduction systems for: (1) finding chitin, (2) adhering to chitinaceous substrata, (3) degrading the chitin to oligosaccharides, (4) transporting the oligosaccharides to the cytoplasm, and (5) catabolizing the transport products to fructose-6-P, acetate and NH(3). The proteins and enzymes are located extracellularly, in the cell envelope, the periplasmic space, the inner membrane and the cytoplasm. In addition to these levels of complexity, the various components of these systems appear to be carefully coordinated by intricate regulatory mechanisms.     

The biogeography of abundant and rare bacterioplankton in the lakes and reservoirs of China

Bacteria play key roles in the ecology of both aquatic and terrestrial ecosystems; however, little is known about their diversity and biogeography, especially in the rare microbial biosphere of inland freshwater ecosystems. Here we investigated aspects of the community ecology and geographical distribution of abundant and rare bacterioplankton using high-throughput sequencing and examined the relative influence of local environmental variables and regional (spatial) factors on their geographical distribution patterns in 42 lakes and reservoirs across China. Our results showed that the geographical patterns of abundant and rare bacterial subcommunities were generally similar, and both of them showed a significant distance–decay relationship. This suggests that the rare bacterial biosphere is not a random assembly, as some authors have assumed, and that its distribution is most likely subject to the same ecological processes that control abundant taxa. However, we identified some differences between the abundant and rare groups as both groups of bacteria showed a significant positive relationship between sites occupancy and abundance, but the abundant bacteria exhibited a weaker distance–decay relationship than the rare bacteria. Our results implied that rare subcommunities were mostly governed by local environmental variables, whereas the abundant subcommunities were mainly affected by regional factors. In addition, both local and regional variables that were significantly related to the spatial variation of abundant bacterial community composition were different to those of rare ones, suggesting that abundant and rare bacteria may have discrepant ecological niches and may play different roles in natural ecosystems.     

Squid-derived chitin oligosaccharides are a chemotactic signal during colonization by Vibrio fischeri

Chitin, a polymer of N-acetylglucosamine (GlcNAc), is noted as the second most abundant biopolymer in nature. Chitin serves many functions for marine bacteria in the family Vibrionaceae ("vibrios"), in some instances providing a physical attachment site, inducing natural genetic competence, and serving as an attractant for chemotaxis. The marine luminous bacterium Vibrio fischeri is the specific symbiont in the light-emitting organ of the Hawaiian bobtail squid, Euprymna scolopes. The bacterium provides the squid with luminescence that the animal uses in an antipredatory defense, while the squid supports the symbiont's nutritional requirements. V. fischeri cells are harvested from seawater during each host generation, and V. fischeri is the only species that can complete this process in nature. Furthermore, chitin is located in squid hemocytes and plays a nutritional role in the symbiosis. We demonstrate here that chitin oligosaccharides produced by the squid host serve as a chemotactic signal for colonizing bacteria. V. fischeri uses the gradient of host chitin to enter the squid light organ duct and colonize the animal. We provide evidence that chitin serves a novel function in an animal-bacterial mutualism, as an animal-produced bacterium-attracting synomone.     

Comparative growth rates of various rumen bacteria in clarified rumen fluid from cows and sheep fed different diets.

Pure cultures of strains of different species of rumen bacteria were grown in filter-sterilized rumen fluid supplemented with glucose, bicarbonate, and reducing agent (cysteine and sulfide). Growth rates were determined in a series of experiments. Strains of species most abundant in the rumen grew more rapidly than strains of less abundant bacteria. Ammonia, amino acids, and peptides increased growth rates to some extent, but the greatest stimulatory effect for less abundant bacteria was provided by other factors, present in yeast extract. Factors released from lysates of mixed rumen microbes stimulated growth, but their rate of release was slow. It was concluded that, besides energy and nitrogen sources, growth factors of an as-yet-undetermined nature probably play an important role in determining the predominance of different bacterial species in the rumen.     

Bacteria isolated from rock art paintings: the case of Atlanterra shelter (south Spain).

The Sierra de la Plata is an Aljibe yellow sandstone formation from the Acheulian period. There are a few shelters, some of them with rock art paintings. The most representative one, and subjected to anthropogenic pressure, is that of Atlanterra, situated in a residential area. This shelter contains some rock art paintings made with iron oxides. The bacteria present in these paintings were isolated and identified using an automatic method: fatty acid methyl esters profiling. Most of the bacteria belong to the Bacillus genus, B. megaterium being the most abundant species. The isolated strains are able to reduce hematite. This is significant due to the fact that Fe(III)-(hydr)oxides are the most abundant pigments in rock art.     

A protocol for the simultaneous identification of chitin-containing particles and their associated bacteria

Chitin is the second most abundant polymer on Earth, playing a crucial role in the biogeochemical cycles. A core issue for studying its processing in aquatic systems is the identification and enumeration of chitin-containing particles and organisms, ideally in a manner that can be directly linked to bulk chitin quantification. The aim of this study was the development of such a technique. We successfully combined the methodology of bulk chitin determination using wheat germ agglutinin (FITC-WGA) for staining chitin-containing particles and organisms along with CARD-FISH staining of either chitin-containing eukaryotic cells or bacteria associated with them. Environmental chitin staining was successfully applied to natural water samples. Fungal hyphae, diatoms, and dinoflagellates, sestonic aggregates and chitin-containing structures derived from metazoa were observed. Also, hybridized bacteria attached to chitinaceous debris were clearly visualized. Finally, as proof of principle, cultured yeast cells were simultaneously-targeted by FITC-WGA and the EUK516 probe without exhibiting any interference between both stains. The presented approach appears as a powerful tool to evaluate the contribution of different size classes and organisms to chitin production and consumption, opening the possibility for application of single-cell approaches targeting the ecophysiology of chitin transformations in aquatic systems.     

Sodium, an Obligate Growth Requirement for Predominant Rumen Bacteria

Sodium is an obligate growth requirement for most currently recognized predominant species of rumen bacteria. The isoosmotic deletion of Na(+) from a nutritionally adequate defined medium completely eliminated growth of most species. Growth yields and rates were both a function of Na(+) concentration for Na(+)-requiring species, and Na(+) could not be replaced by Rb(+), Li(+), or Cs(+) when these ions were substituted for Na(+) at a concentration equivalent to an Na(+) concentration that supported abundant growth. Li(+), Cs(+), or Rb(+) was toxic at an Na(+)-replacing concentration (15 mM) but not at a K(+)-replacing concentration (0.65 mM). K(+) was also an obligate growth requirement for rumen bacteria in media containing Na(+) and K(+) as major monovalent cations, but K(+) could be replaced, for most species, by Rb(+). The quantities of Na(+) that support rapid and abundant growth of Na(+)-requiring rumen bacteria show that these organisms are slight halophiles. A growth requirement for Na(+) appears more frequent among nonmarine bacteria than has been previously believed.     

Enumeration and presumptive identification of some functional groups of bacteria in the rumen of dairy cows fed grass silage-based diets

Abstract Samples of rumen ingesta from two rumen-fistulated dairy cows fed grass silage-based diets were examined for numbers and types of bacteria that developed colonies on rumen fluid-agar media designated to support the growth of (a) a wide range of species, (b) cellulolytic bacteria, (c) lactate-fermenting bacteria, (d) non-fermentative bacteria. The most numerous species was Bacteroides ruminicola followed by Butyrivibrio fibrisolvens . The most abundant cellulolytic species were Eubacterium cellulosolvens and Ruminococcus flavefaciens. Megasphaera elsdenii and Selenomonas ruminantium were important lactate fermenters but an unidentified bacterium that grew poorly on maintenance medium was by far the most numerous among bacteria isolated from lactate-containing medium. One strain remained sufficiently viable to show that it fermented lactate to propionate and acetate.     

Comparative growth rates of various rumen bacteria in clarified rumen fluid from cows and sheep fed different diets.

Pure cultures of strains of different species of rumen bacteria were grown in filter-sterilized rumen fluid supplemented with glucose, bicarbonate, and reducing agent (cysteine and sulfide). Growth rates were determined in a series of experiments. Strains of species most abundant in the rumen grew more rapidly than strains of less abundant bacteria. Ammonia, amino acids, and peptides increased growth rates to some extent, but the greatest stimulatory effect for less abundant bacteria was provided by other factors, present in yeast extract. Factors released from lysates of mixed rumen microbes stimulated growth, but their rate of release was slow. It was concluded that, besides energy and nitrogen sources, growth factors of an as-yet-undetermined nature probably play an important role in determining the predominance of different bacterial species in the rumen.     

The coral core microbiome identifies rare bacterial taxa as ubiquitous endosymbionts

Despite being one of the simplest metazoans, corals harbor some of the most highly diverse and abundant microbial communities. Differentiating core, symbiotic bacteria from this diverse host-associated consortium is essential for characterizing the functional contributions of bacteria but has not been possible yet. Here we characterize the coral core microbiome and demonstrate clear phylogenetic and functional divisions between the micro-scale, niche habitats within the coral host. In doing so, we discover seven distinct bacterial phylotypes that are universal to the core microbiome of coral species, separated by thousands of kilometres of oceans. The two most abundant phylotypes are co-localized specifically with the corals'' endosymbiotic algae and symbiont-containing host cells. These bacterial symbioses likely facilitate the success of the dinoflagellate endosymbiosis with corals in diverse environmental regimes.     

土壤细菌类克隆群落及其结构的生态学特征

以16SrDNA分析方法为基础,获得来自不同土壤环境的细菌克隆群落（Cloning community),并分析了这些土壤细菌群落结构特征,在不同土壤环境中,细菌种类非常丰富,但其多样性将受到植被,土壤水分或土壤层次等因子的影响,表层土壤环境中细菌种类最丰富,多样性最高,且基因型中无明显的优势类群,不同土壤环境间细菌群落的相似性好低,表明群落结构以及空间隔离的复杂性。     

Isolation and characterization of marine oligotrophic bacteria

A significant part of the world ocean is characterized by low absolute nutrients and chlorophyll concentrations. In these oligotrophic environments, bacteria are very abundant and play a vital role in the remineralization of the dissolved organic matter. Bacteria adapted to oligotrophic waters differ from those adapted to richer environments by some genetic and metabolic characteristics. Culture techniques in bacteriology are based on rich media and do not allow the growth of most marine bacteria. New techniques have been developed for the culture of oligotrophic bacteria, which allow to isolate unknown bacteria. Pelagibacter ubique and Sphingopyxis alaskensis belong to these bacteria recently isolated from the marine environment and their study yielded better understanding of how marine bacteria adapt to oligotrophic conditions.     

Unraveling the camel rumen microbiome through metaculturomics approach for agriculture waste hydrolytic potential

Archives of Microbiology - Cellulose is the most abundant natural polymer present on Earth in the form of agriculture waste. Hydrolysis of agriculture waste for simple fermentable reducing sugars...     

Bacteriological composition and structure of granular sludge adapted to different substrates.

The bacteriological composition and ultrastructure of mesophilic granular methanogenic sludge from a large-scale Upflow Anaerobic Sludge Blanket reactor treating wastewater from a sugar plant and of sludge granules adapted to ethanol and propionate were studied by counting different bacterial groups and by immunocytochemical methods. Propionate-grown granular sludge consisted of two types of clusters, those of a rod-shaped bacterium immunologically related to Methanothrix soehngenii and those consisting of two different types of bacteria with a specific spatial orientation. One of these bacteria reacted with antiserum against Methanobrevibacter arboriphilus AZ, whereas the other is most likely a propionate-oxidizing bacterium immunologically unrelated to Syntrophobacter wolinii. Sludge granules obtained from the large-scale Upflow Anaerobic Sludge Blanket reactor and granules cultivated on ethanol did not show the typical spatial orientation of bacteria. Examination of the bacterial composition of the three types of granules by light and electron microscopy, the most-probable-number method, and by isolations showed that M. arboriphilus and M. soehngenii were the most abundant hydrogenotrophic and acetoclastic methanogens in propionate-grown sludge. Methanospirillum hungatei and Methanosarcina barkeri predominated in ethanol-grown granules, whereas many morphotypes of methanogens were abundant in granules from the full-scale reactor.