Biodegradation of epoxy residues by endophytic bacteria Staphylococcus lentus (KARE_P3) A sustainable approach to plastic pollution

Background: Candida infection currently presents a major problem. The natural products from endophytic bacteria are thought to have a strong potential for treatment. Objectives: The present study aimed to isolate endophytic bacteria from Dryopteris uniformis, its identification, and investigation of their anticandidal activity and confirm it. Methods: The isolated endophytic bacteria from D. uniformis were identified by using 16S rRNA gene sequencing. The anticandidal assay of endophytic bacteria was performed by using the patch method. Endophytic bacteria were successively fractionated by using different polarity solvents. The anticandidal activity of each solvent fraction was evaluated by using the disc diffusion method and was confirmed by scanning electron microscopy. Results: Fifty-one endophytic bacteria were isolated from the lead and stem/root of D. uniformis and screened for anticandidal activity against five Candida species, Candida saitoana (KACC 41238), C. albicans (KACC 30062), C. albicans (KACC 30003), C. glabrata (KBNO6P00368) and C. glochares (KACC 30061). Among these, six endophytic bacteria exhibited strong anticandidal activity with an inhibition zone diameter between 9.29 and 47.67 mm against four Candida species; these bacteria were identified as Burkholderia sp. UR 1-07 (DUS14), Staphylococcus sp. WW60 (DUS56), Bacillus sp. cryopeg (DUS59), Paenibacillus sp. rif200865 (DUL128), Staphylococcus warneri (DUS130), and Bacillus psychrodurans (DUS131) using 16S rRNA gene sequencing. The minimum inhibitory concentration (MIC) of the butanol fraction of the selected endophytic bacteria, Burkholderia sp., was 250 µg/mL and the minimum fungicidal concentration (MFC) was 500 µg/mL. Scanning electron microscopy result indicated that, MIC of promising endophytic bacteria Burkholderia sp. destroyed the target Candida cells. Conclusions: This study demonstrated anticandidal potential of endophytic bacteria derived from D. uniformis.

Plant endophytic bacteria play important roles in plants’ growth and resistance to stress. It is important to characterize endophytic bacteria to be able to understand their benefits. Matrix-assisted laser desorption ionization–time of flight mass spectrometry (MALDI-TOF MS) has become a powerful technique for bacterial identification due to its high throughput and simple procedures. In this study, the endophytic bacteria separated from Populus (the leaves, roots and stems of Populus tomentosa Carrière; stems of Populus nigra Linn. var. nigra; and stems of Populus canadensis Moench) were identified and classified based on MALDI-TOF MS data and 16S rRNA gene sequencing. The sampling and preparation of bacteria were optimized to obtain meaningful protein mass fingerprints. The composite correlation index (CCI) values of the inter-genera and inter-species protein mass fingerprints demonstrated sufficient differences between the strains. In the CCI value matrix for ten species in the same genus, all the CCI values were less than 0.5. Among the species, 95.6% of all the CCI values were less than 0.5. After data processing, the classification capacity of the protein mass fingerprints was verified using inter-specific and inter-generic PCoA. To compare different methods’ potential for differentiation and phylogenetic analysis, a dendrogram of the MS profiles and a phylogenetic tree based on the 16S rRNA gene sequences were constructed using 61 endophytic bacteria found in Populus. The clustering and grouping results show that the phylogenetic analysis based on MALDI-TOF MS is similar to that based on 16S rRNA gene sequencing. This study provides a valuable reference for differentiating and identifying endophytic bacteria according to their protein mass fingerprints.

<i>Leptotrichia amnionii</i>and the Female Reproductive Tract

Clove (Syzygium aromaticum L.) is one type of spice plant that has high antioxidant content because of the high eugenol compounds. However, iso-lating these bioactive compounds require a significant amount of biomass. A known alternative solution to overcome the problems is through the utiliza-tion of endophytic bacteria in clove leaves. Endophytic cloves leaf bacteria can be a good antioxidant resource. Endophytic bacteria are bacteria that grow in plant tissues that is not pathogenic, which can replace these plants. The aim of this study is isolating endophytic bacterial from clove leaves, screening endophytic bacteria, determining potential endophytic bacteria as producer antioxidant compounds, and identifying potential isolate using 16S rRNA. This study used endophytic bacteria isolated from clove leaves (Syzygium aromaticum L.). Antioxidant activity determined using DPPH method. It was founded 7 isolates of endophytic bacteria namely WDY1, WDY2, WDY3, WDY4, WDY5, WDY6, and WDY7. The isolate WDY6 shows the highest antioxidant activity. WDY6 isolate is identical to Staphylococcus sp. with a 100% similarity. Staphylococcus sp. has the highest antioxidant activ-ity in the stationary phase. The content of chemical compounds from WDY6 isolates is pyrazine that belongs to alkaloids.

According to the Food and Agricultural Organization (FAO), “global agricultural production needs to increase by 70% and double in developing countries by 2050 to meet the demand of 9 billion people”. The major challenge all countries are currently facing in the world is food security. It is connected to two inseparable components, namely, land and water. In a context of agro-ecological transition, many actors including those of research are mobilized to develop sustainable solutions. These include the use of biofertilizers of microbial origin. Microbial biofertilizers are a sustainable alternative to currently widely used inputs. In contrast to these, biofertilizers ensure plant productivity and conservation of water, soil and biodiversity resources. Moreover, their use does not impact human health. Plants can be described as complex micro-ecosystems to which the different habitats are exploited by a wide variety of bacteria. Endophytes are non-pathogenic organisms that perform part or all of their life cycle within plant tissues. Endophytic bacteria are likely to have beneficial effects similar to the known effects of plant growth-promoting rhizobacteria (PGPR). A number of studies evoke the interest of endophytic bacteria, but only a few bring up the topic of seed endophytic bacteria. Hence, seeds are essential tools for agricultural production, as well as potential supports for endophytic bacteria. This chapter aims to highlight the potentialities of the seed-borne endophytic bacteria for agricultural use due to their remarkable abilities (survival in extreme conditions, motility, competitive advantage, vertical transmission, contribution to germination, growth-promoting effects, biocontrol abilities). The examples mentioned for the different kind of cultures (market gardening, big cultures, forage crops, niche market cultures) demonstrate the relevance of agricultural purposes.KeywordsEndophytic bacteriaBiofertilizersBiopesticidesAgro-ecologyPGPR

Endophytes are an important constituent of sustainable agriculture because of their ability to produce a large number of agriculturally important metabolites. A salt-tolerant fluorescent green pigment-producing endophytic bacterium was isolated on 2.5% NaCl-supplemented nutrient agar from the leaf samples of Zanthoxylum alatum Roxb. The isolate Z1B4 was identified as Pseudomonas fluorescens based on morphological features, fatty acid methyl ester analysis, biochemical tests, and 16S rRNA gene sequencing. P. fluorescens Z1B4 showed positive results for tricalcium phosphate solubilization; 1-aminocyclopropane-1-carboxylate (ACC) deaminase activity; and production of auxins, siderophores, hydrogen cyanide, and ammonia. P. fluorescens Z1B4 also showed strong antagonistic activity against Curvularia lunata (MTCC 283), Fusarium verticillioides (MTCC 3322), and Alternaria alternata (MTCC 1362) and exhibited stress tolerance to a wide range of temperature and pH and concentrations of NaCl and calcium salts. Under natural conditions, following inoculation with the isolate Z1B4, a significant increase in the growth of pea and maize test plants in pots was observed compared to that of uninoculated control plants. The rifampicin-resistant mutant Z1B4Rif was recovered from the roots, shoots, and leaves of the test plants, indicating that the isolated endophytic bacterium can grow well within different plant tissues. The present study indicated that the endophytic bacterium P. fluorescens Z1B4 can be used as a bacterial inoculant in stressed environments for sustainable agriculture.

Endophytic bacteria are microorganisms that live in plant tissues and some of them contribute to nitrogen fixation for plants. This study aimed to isolate and identify endophytic bacteria from mangroves of Kutang Beach, Lamongan, which potentially as nitrogen fixing bacteria. Bacterial Isolates were used as candidates for biofertilizers. Leaves samples were taken from 10 sampling points. Bacterial isolation was initiated by sterilizing the surface of the leaves sample and grinding it aseptically. Isolation was carried out with a pour plate method on Nutrient Agar medium. Screening for endophytic bacteria's potential as N-fixing agent was carried out by growing the bacterial isolates on a semi-solid Nitrogen Free Bromothymol Blue (NFB) medium. The isolates that produced a positive reaction with a change in the color of the medium to blue were then subjected to macroscopic (shape, color, elevation, and the edge of the colony) and microscopic observations (Gram stain and bacterial cell measurements). The isolates showed the fastest change in the color of the medium were identified by the molecular marker of the 16S rRNA gene. The data obtained were analyzed descriptively. As many as 20 isolates were obtained from the mangroves of Kutang Lamongan Beach, and ten isolates of twenty potentially as nitrogen-fixing bacteria. The ten nitrogen-fixing bacteria isolates had varying macroscopic characteristics. The microscopic characteristics showed that eight isolates had Gram-positive bacilli, and two isolates were Gram-negative with varying bacterial sizes. Based on the 16S rRNA gene sequence, the most potential of nitrogen-fixing bacteria was LMG II-14 isolate and identified as Paenibacillus alvei LMG II-14 with 99.36% similarity to Paenibacillus alvei strain DSM 29 based on the NCBI database. The ten nitrogen fixing isolates that have been obtained can later be used as candidates for biofertilizer composition, especially Paenibacillus alvei LMG II-14.

Bacterial communities play an important role in mangrove ecosystems. In order to gain information on the bacterial communities in mangrove species and rhizospheres grown in Zhangjiangkou National Mangrove Nature Reserve, this study collected root, branch, and leaf samples from five mangrove species as well as rhizosphere and non-rhizosphere samples and analyzed the community structure of endophytic bacteria and bacteria in rhizosphere and non-rhizosphere using Illumina high-throughput sequencing technique. Bacteria in 52 phyla, 64 classes, 152 orders, 295 families, and 794 genera were identified, which mainly belonged to Proteobacteria, Cyanobacteria, Actinobacteria, Firmicutes, Bacteroidetes, Fusobacteria, and Nitrospirota. At each taxonomic level, the community structure of the rhizosphere bacteria varied slightly with mangrove species, but endophytic bacteria differed greatly with plant species. The diversity indices of endophytic bacteria in branch and leaf samples of Acanthus ilicifolius were significantly lower, and endophytic bacteria in the plant tissues had higher abundance in the replication/repair and translation Clusters of Orthologous Genes functional categories but lower abundance in the carbohydrate metabolism category. This study helps to understand the community structure and diversity characteristics of endophytic and rhizosphere bacteria in different mangrove plants. Provide a theoretical basis for in-depth research on the functions of mangrove ecosystems.

Endophytic bacteria are ubiquitous in most plant species, residing latently or actively colonizing plant tissues locally as well as systemically. Several definitions have been proposed for endophytic bacteria; in this review endophytes will be defined as those bacteria that can be isolated from surface-disinfested plant tissue or extracted from within the plant, and that do not visibly harm the plant. While this definition does not include nonextractable endophytic bacteria, it is a practical definition based on experimental limitations and is inclusive of bacterial symbionts, as well as internal plant-colonizing nonpathogenic bacteria with no known beneficial or detrimental effects on colonized plants. Historically, endophytic bacteria have been thought to be weakly virulent plant pathogens but have recently been discovered to have several beneficial effects on host plants, such as plant growth promotion and increased resistance against plant pathogens and parasites. In general, endophytic bacteria originate from the epiphytic bacterial communities of the rhizosphere and phylloplane, as well as from endophyte-infested seeds or planting materials. Besides gaining entrance to plants through natural openings or wounds, endophytic bacteria appear to actively penetrate plant tissues using hydrolytic enzymes like cellulase and pectinase. Since these enzymes are also produced by pathogens, more knowledge on their regulation and expression is needed to distinguish endophytic bacteria from plant pathogens. In general, endophytic bacteria occur at lower population densities than pathogens, and at least some of them do not induce a hypersensitive response in the plant, indicating that they are not recognized by the plant as pathogens. Evolutionarily, endophytes appear to be intermediate between saprophytic bacteria and plant pathogens, but it can only be speculated as to whether they are saprophytes evolving toward pathogens, or are more highly evolved than plant pathogens and conserve protective shelter and nutrient supplies by not killing their host. Overall, the endophytic microfloral community is of dynamic structure and is influenced by biotic and abiotic factors, with the plant itself constituting one of the major influencing factors. Since endophytic bacteria rely on the nutritional supply offered by the plant, any parameter affecting the nutritional status of the plant could consequently affect the endophytic community. This review summarizes part of the work being done on endophytic bacteria, including their methodology, colonization, and establishment in the host plant, as well as their role in plant–microbe interactions. In addition, speculative conclusions are raised on some points to stimulate thought and research on endophytic bacteria.Key words: endophytic bacteria, methods, localization, diversity, biological control.

Communities of bacterial endophytes within the rice landraces cultivated in the highlands of northern Thailand were studied using fingerprinting data of 16S rRNA and nifH genes profiling by polymerase chain reaction-denaturing gradient gel electrophoresis. The bacterial communities' richness, diversity index, evenness, and stability were varied depending on the plant tissues, stages of growth, and rice cultivars. These indices for the endophytic diazotrophic bacteria within the landrace rice Bue Wah Bo were significantly the lowest. The endophytic bacteria revealed greater diversity by cluster analysis with seven clusters compared to the endophytic diazotrophic bacteria (three clusters). Principal component analysis suggested that the endophytic bacteria showed that the community structures across the rice landraces had a higher stability than those of the endophytic diazotrophic bacteria. Uncultured bacteria were found dominantly in both bacterial communities, while higher generic varieties were observed in the endophytic diazotrophic bacterial community. These differences in bacterial communities might be influenced either by genetic variation in the rice landraces or the rice cultivation system, where the nitrogen input affects the endophytic diazotrophic bacterial community.

A strain of a novel anaerobic, Gram-stain-negative coccus was isolated from the tongue biofilm of a Thai child. This strain was shown, at the phenotypic level and based on 16S rRNA gene sequencing, to be a member of the genus Veillonella. Comparative analysis of the 16S rRNA, dnaK and rpoB gene sequences indicated that phylogenetically the strain comprised a distinct novel branch within the genus Veillonella. The novel strain showed 99.8, 95.1 and 95.9 % similarity to partial 16S rRNA, dnaK and rpoB gene sequences, respectively, to the type strains of the two most closely related species, Veillonelladispar ATCC 17748T and Veillonellatobetsuensis ATCC BAA-2400T. The novel strain could be discriminated from previously reported species of the genus Veillonella based on partial dnaK and rpoB gene sequencing and average nucleotide identity values. The major acid end-product produced by this strain was acetic acid under anaerobic conditions in trypticase-yeast extract-haemin with 1 % (w/v) glucose or fructose medium. Lactate was fermented to acetic acid and propionic acid. Based on these observations, this strain represents a novel species, for which the name Veillonella infantium sp. nov. is proposed. The type strain is T11011-4T (=JCM 31738T=TSD-88T).

Cymbidium faberi is a representative species of Cymbidium with high ornamental and economic value. Investigating the diversity of C. faberi’s endophytic bacteria not only enriches endophytic bacterial resources, but also provides basic data on orchid-microbe interactions. We investigated the genetic diversity of culturable endophytic bacteria in the roots of wild C. faberi from Tianmu Mountain, Zhejiang Province and C. faberi grown in a greenhouse for one year. Culture-dependent methods were used to isolate endophytic bacteria from the roots of C. faberi. The diversity of these bacteria was investigated using 16S rRNA gene partial sequence analysis. A total of 97 strains were isolated from the interior of wild C. faberi roots. Based on 16S rRNA gene sequences, the 97 isolates were affiliated with 13 genera of Alphaproteobacteria, Betaproteobacteria, Gammaproteobacteria, and Firmicutes. The dominant group was Gammaproteobacteria (86.60%), and the dominant genus was Lelliottia (26.80%). A total of 52 endophytic strains were isolated from the roots of C. faberi grown in the greenhouse. Based on 16S rRNA gene sequences, the 52 isolates were grouped into 9 genera of Alphaproteobacteria, Betaproteobacteria, Gammaproteobacteria and Actinobacteria. The dominant group was Betaproteobacteria (48.08%), and the dominant genus was Herbaspirillum (34.62%). The strain ehR17 was identified as a potential novel species. For C. faberi, the diversity of culturable endophytic bacteria was higher from the wild Tianmu Mountain population than from plants grown in the greenhouse for one year. Community structure of endophytic bacteria was closely related to plant growth environment. 62 生 物 多 样 性 Biodiversity Science 第 23卷

The taxonomy of the genus Campylobacter has changed dramatically since its inception in 1963. At that time the genus comprised just two species. At present, taxa that were once assigned to Campylobacter may belong to one of over 50 species distributed among six genera. Most of these taxa belong to a phylogenetically distinct group referred to as either ribosomal RNA (rRNA) superfamily VI or the epsilon division of the class Proteobacteria. The taxonomic diversity of the group is matched by the diverse habitats in which they may be found, and by the wide range of diseases that they are associated with. Recognition of their clinical and economic importance has resulted in intense interest in the group, and the application of increasingly sophisticated isolation, detection and chemotaxonomic methods continues to elucidate new aspects of their biodiversity. However, despite the advances in new bacterial systematics, there remain a number of important issues concerning the classification of various campylobacterial taxa that require careful consideration. Ultimately, these issues are relevant to many working in the field of applied microbiology, including clinicians, veterinarians, epidemiologists and taxonomists. The purpose of this article is briefly to review the major developments in the taxonomy of Campylobacter from its inception to the present day; summarize the most recent changes in the field; analyse current topical issues of special relevance to applied microbiologists, including identification of the bacteria; and speculate on future prospects for campylobacterial taxonomy.

Enhanced growth and nodulation of pigeon pea by co-inoculation of Bacillus strains with Rhizobium spp.

The endophytic bacteria in the seeds of rice plants (Oryza sativa, cultivar Kinuhikari) cultivated on an experimental plot adjacent to a paddy field were studied as the seeds matured by comparing them with the bacteria on the surface of the seeds. Endophytic and surface bacteria were isolated using a nutrient broth and a diluted nutrient broth agar medium. The isolates were identified based on 16S rRNA gene sequences. Three genera (Paenibacillus, Acidovorax and Pantoea) and 2 genera (Stenotrophomonas and Rhizobium) were specific to the inside and to the surface of the seeds, respectively. Six genera (Bacillus, Curtobacterium, Methylobacterium, Sphingomonas, Xanthomonas and Micrococcus) were common to both the inside and the surface. As the seed matured, the flora of culturable endophytic bacteria changed in a different manner from that of culturable surface bacteria. More isolates tolerant of high osmotic pressure were found among the endophytes than among the surface bacteria, especially at the later stages of the maturation process. An increasing number of endophytic isolates exhibited amylase activity at the later stages.