Bacterial succession within an ephemeral hypereutrophic mojave desert playa lake

USGS Publications Warehouse

Navarro, J.B.; Moser, D.P.; Flores, A.; Ross, C.; Rosen, Michael R.; Dong, H.; Zhang, G.; Hedlund, B.P.

2009-01-01

Ephemerally wet playas are conspicuous features of arid landscapes worldwide; however, they have not been well studied as habitats for microorganisms. We tracked the geochemistry and microbial community in Silver Lake playa, California, over one flooding/desiccation cycle following the unusually wet winter of 2004-2005. Over the course of the study, total dissolved solids increased by 10-fold and pH increased by nearly one unit. As the lake contracted and temperatures increased over the summer, a moderately dense planktonic population of 1 ?????106 cells ml-1 of culturable heterotrophs was replaced by a dense population of more than 1????????109 cells ml-1, which appears to be the highest concentration of culturable planktonic heterotrophs reported in any natural aquatic ecosystem. This correlated with a dramatic depletion of nitrate as well as changes in the microbial community, as assessed by small subunit ribosomal RNA gene sequencing of bacterial isolates and uncultivated clones. Isolates from the early-phase flooded playa were primarily Actinobacteria, Firmicutes, and Bacteroidetes, yet clone libraries were dominated by Betaproteobacteria and yet uncultivated Actinobacteria. Isolates from the late-flooded phase ecosystem were predominantly Proteobacteria, particularly alkalitolerant isolates of Rhodobaca, Porphyrobacter, Hydrogenophaga, Alishwenella, and relatives of Thauera; however, clone libraries were composed almost entirely of Synechococcus (Cyanobacteria). A sample taken after the playa surface was completely desiccated contained diverse culturable Actinobacteria typically isolated from soils. In total, 205 isolates and 166 clones represented 82 and 44 species-level groups, respectively, including a wide diversity of Proteobacteria, Bacteroidetes, Actinobacteria, Firmicutes, Gemmatimonadetes, Acidobacteria, and Cyanobacteria. ?? 2008 Springer Science+Business Media, LLC.

Diversity of bacteria in surface ice of Austre Lovénbreen glacier, Svalbard.

PubMed

Zeng, Yin-Xin; Yan, Ming; Yu, Yong; Li, Hui-Rong; He, Jian-Feng; Sun, Kun; Zhang, Fang

2013-05-01

Two 16S rRNA gene clone libraries Cores 1U and 2U were constructed using two ice core samples collected from Austre Lovénbreen glacier in Svalbard. The two libraries yielded a total of 262 clones belonging to 59 phylotypes. Sequences fell into 10 major lineages of the domain Bacteria, including Proteobacteria (alpha, beta, gamma and delta subdivisions), Bacteroidetes, Actinobacteria, Firmicutes, Acidobacteria, Deinococcus-Thermus, Chloroflexi, Planctomycetes, Cyanobacteria and candidate division TM7. Among them, Bacteroidetes, Actinobacteria, Alphaproteobacteria and Cyanobacteria were most abundant. UniFrac data showed no significant differences in community composition between the two ice cores. A total of nineteen bacterial strains from the genera Pseudoalteromonas and Psychrobacter were isolated from the ice cores. Phylogenetic and phenotypic analyses revealed a close relationship between the ice core isolates and bacteria in marine environments, indicating a wide distribution of some bacterial phylotypes in both terrestrial and marine ecosystems.

Community structure and elevational diversity patterns of soil Acidobacteria.

PubMed

Zhang, Yuguang; Cong, Jing; Lu, Hui; Li, Guangliang; Qu, Yuanyuan; Su, Xiujiang; Zhou, Jizhong; Li, Diqiang

2014-08-01

Acidobacteria is one of the most dominant and abundant phyla in soil, and was believed to have a wide range of metabolic and genetic functions. Relatively little is known about its community structure and elevational diversity patterns. We selected four elevation gradients from 1000 to 2800 m with typical vegetation types of the northern slope of Shennongjia Mountain in central China. The vegetation types were evergreen broadleaved forest, deciduous broadleaved forest, coniferous forest and sub-alpine shrubs. We analyzed the soil acidobacterial community composition, elevational patterns and the relationship between Acidobacteria subdivisions and soil enzyme activities by using the 16S rRNA meta-sequencing technique and multivariate statistical analysis. The result found that 19 known subdivisions as well as an unclassified phylotype were presented in these forest sites, and Subdivision 6 has the highest number of detectable operational taxonomic units (OTUs). A significant single peak distribution pattern (P<0.05) between the OTU number and the elevation was observed. The Jaccard and Bray-Curtis index analysis showed that the soil Acidobacteria compositional similarity significantly decreased (P<0.01) with the increase in elevation distance. Mantel test analysis showed the most of the soil Acidobacteria subdivisions had the significant relationship (P<0.01) with different soil enzymes. Therefore, soil Acidobacteria may be involved in different ecosystem functions in global elemental cycles. Partial Mantel tests and CCA analysis showed that soil pH, soil temperature and plant diversity may be the key factors in shaping the soil Acidobacterial community structure. Copyright © 2014. Published by Elsevier B.V.

Taxonomic hierarchy of the phylum Firmicutes and novel Firmicutes species originated from various environments in Korea.

PubMed

Seong, Chi Nam; Kang, Joo Won; Lee, Ji Hee; Seo, So Yeon; Woo, Jung Jae; Park, Chul; Bae, Kyung Sook; Kim, Mi Sun

2018-01-01

This study assessed the taxonomic hierarchy of the phylum Firmicutes as well as elucidated the isolation and classification states of novel Firmicutes species isolated from Korean territory. The hierarchical classification system of the phylum Firmicutes has been developed since 1872 when the genus Bacillus was first reported and has been generally adopted since 2001. However, this taxonomic hierarchy is still being modified. Until Feb. 2017, the phylum Firmicutes consisted of seven classes (Bacilli, Clostridia, Erysipelotrichia, Limnochordia, Negativicutes, Thermolithobacteria, and Tissierellia), 13 orders, 45 families, and 421 genera. Firmicutes species isolated from various environments in Korea have been reported from 2000, and 187 species have been approved as of Feb. 2017. All Firmicutes species were affiliated with three classes (Bacilli, Clostridia, and Erysipelotrichia), four orders (Bacillales, Lactobacillales, Clostridiales, and Erysipelotrichales), 17 families, and 54 genera. A total of 173 species belong to the class Bacilli, of which 151 species were affiliated with the order Bacillales and the remaining 22 species with the order Lactobacillales. Twelve species belonging to the class Clostridia were affiliated within only one order, Clostridiales. The most abundant family was Bacillaceae (67 species), followed by the family Paenibacillaceae (56 species). Thirteen novel genera were created using isolates from the Korean environment. A number of Firmicutes species were isolated from natural environments in Korean territory. In addition, a considerable number of species were isolated from artificial resources such as fermented foods. Most Firmicutes species, belonging to the families Bacillaceae, Planococcaceae, and Staphylococcaceae, isolated from Korean fermented foods and solar salterns were halophilic or halotolerant. Firmicutes species were isolated from the whole territory of Korea, especially large numbers from Provinces Gyeonggi, Chungnam, and

Persistence of the dominant soil phylum Acidobacteria by trace gas scavenging

PubMed Central

Greening, Chris; Carere, Carlo R.; Rushton-Green, Rowena; Harold, Liam K.; Hards, Kiel; Taylor, Matthew C.; Morales, Sergio E.; Stott, Matthew B.; Cook, Gregory M.

2015-01-01

The majority of microbial cells in global soils exist in a spectrum of dormant states. However, the metabolic processes that enable them to survive environmental challenges, such as nutrient-limitation, remain to be elucidated. In this work, we demonstrate that energy-starved cultures of Pyrinomonas methylaliphatogenes, an aerobic heterotrophic acidobacterium isolated from New Zealand volcanic soils, persist by scavenging the picomolar concentrations of H2 distributed throughout the atmosphere. Following the transition from exponential to stationary phase due to glucose limitation, the bacterium up-regulates by fourfold the expression of an eight-gene operon encoding an actinobacteria-type H2-uptake [NiFe]-hydrogenase. Whole-cells of the organism consume atmospheric H2 in a first-order kinetic process. Hydrogen oxidation occurred most rapidly under oxic conditions and was weakly associated with the cell membrane. We propose that atmospheric H2 scavenging serves as a mechanism to sustain the respiratory chain of P. methylaliphatogenes when organic electron donors are scarce. As the first observation of H2 oxidation to our knowledge in the Acidobacteria, the second most dominant soil phylum, this work identifies new sinks in the biogeochemical H2 cycle and suggests that trace gas oxidation may be a general mechanism for microbial persistence. PMID:26240343

Pheno- and Genotyping of Hopanoid Production in Acidobacteria

PubMed Central

Damsté, Jaap S. Sinninghe; Rijpstra, W. Irene C.; Dedysh, Svetlana N.; Foesel, Bärbel U.; Villanueva, Laura

2017-01-01

Hopanoids are pentacyclic triterpenoid lipids synthesized by different bacterial groups. Methylated hopanoids were believed to be exclusively synthesized by cyanobacteria and aerobic methanotrophs until the genes encoding for the methylation at the C-2 and C-3 position (hpnP and hpnR) were found to be widespread in the bacterial domain, invalidating their use as specific biomarkers. These genes have been detected in the genome of the Acidobacterium “Ca. Koribacter versatilis,” but our knowledge of the synthesis of hopanoids and the presence of genes of their biosynthetic pathway in other member of the Acidobacteria is limited. We analyzed 38 different strains of seven Acidobacteria subdivisions (SDs 1, 3, 4, 6, 8, 10, and 23) for the presence of C30 hopenes and C30+ bacteriohopane polyols (BHPs) using the Rohmer reaction. BHPs and/or C30 hopenes were detected in all strains of SD1 and SD3 but not in SD4 (excepting Chloracidobacterium thermophilum), 6, 8, 10, and 23. This is in good agreement with the presence of genes required for hopanoid biosynthesis in the 31 available whole genomes of cultivated Acidobacteria. All genomes encode the enzymes involved in the non-mevalonate pathway ultimately leading to farnesyl diphosphate but only SD1 and 3 Acidobacteria and C. thermophilum encode all three enzymes required for the synthesis of squalene, its cyclization (shc), and addition and modification of the extended side chain (hpnG, hpnH, hpnI, hpnJ, hpnO). In almost all strains, only tetrafunctionalized BHPs were detected; three strains contained variable relative abundances (up to 45%) of pentafunctionalized BHPs. Only “Ca. K. versatilis” contained methylated hopanoids (i.e., 2,3-dimethyl bishomohopanol), although in low (<10%) amounts. These genes are not present in any other Acidobacterium, consistent with the absence of methylated BHPs in the other examined strains. These data are in agreement with the scattered occurrence of methylated BHPs in other

The effect of anaerobic-aerobic and feast-famine cultivation pattern on bacterial diversity during poly-β-hydroxybutyrate production from domestic sewage sludge.

PubMed

Liu, Changli; Liu, Di; Qi, Yingjie; Zhang, Ying; Liu, Xi; Zhao, Min

2016-07-01

The main objective of this work was to investigate the influence of different oxygen supply patterns on poly-β-hydroxybutyrate (PHB) yield and bacterial community diversity. The anaerobic-aerobic (A/O) sequencing batch reactors (SBR1) and feast-famine (F/F) SBR2 were used to cultivate activated sludge to produce PHB. The mixed microbial communities were collected and analyzed after 3 months cultivation. The PHB maximum yield was 64 wt% in SBR1 and 53 wt% in SBR2. Pyrosequencing analysis 16S rRNA gene of two microbial communities indicated there were nine and four bacterial phyla in SBR1 and SBR2, respectively. Specifically, Proteobacteria (36.4 % of the total bacterial community), Actinobacteria (19.7 %), Acidobacteria (14.1 %), Firmicutes (4.4 %), Bacteroidetes (1.7 %), Cyanobacteria/Chloroplast (1.5 %), TM7 (0.8 %), Gemmatimonadetes (0.2 %), and Nitrospirae (0.1 %) were present in SBR1. Proteobacteria (94.2 %), Bacteroidetes (2.9 %), Firmicutes (1.9 %), and Actinobacteria (0.7 %) were present in SBR2. Our results indicated the SBR1 fermentation system was more stable than that of SBR2 for PHB accumulation.

Structure, Function and Diversity of the Healthy Human Microbiome

DTIC Science & Technology

2012-06-14

1 4 J U N E 2 0 1 2 Macmillan Publishers Limited. All rights reserved©2012 Phyla Firmicutes Actinobacteria Bacteroidetes Proteobacteria Fusobacteria...ra y– C ur tis ) Actinobacteria | Actinobacteria Bacteroidetes|Bacteroidia Firmicutes|Bacilli Firmicutes|Negativicutes Proteobacteria|Gammaproteobacteria...spp. dominating all three and correlating in abundance. However, Lactobacillus varied inversely with the Actinobacteria and Bacteroidetes (see Supplemen

A culture-based study of the bacterial communities within the guts of nine longicorn beetle species and their exo-enzyme producing properties for degrading xylan and pectin.

PubMed

Park, Doo-Sang; Oh, Hyun-Woo; Jeong, Won-Jin; Kim, Hyangmi; Park, Ho-Yong; Bae, Kyung Sook

2007-10-01

In this study, bacterial communities within the guts of several longicorn beetles were investigated by a culture-dependent method. A total of 142 bacterial strains were isolated from nine species of longicorn beetle, including adults and larvae. A comparison of their partial 16S rRNA gene sequences showed that most of the bacteria constituting the gut communities can typically be found in soil, plants and the intestines of animals, and approximately 10% were proposed as unreported. Phylogenetic analysis demonstrated that the bacterial species comprised 7 phyla, and approximately half were Gammaproteobacteria. Actinobacteria were the second most populous group (19%), followed by Firmicutes (13%) and Alphaproteobacteria (11%). Betaproteobacteria, Flavobacteria, and Acidobacteria were minor constituents. The taxonomic compositions of the isolates were variable according to the species of longicorn beetle. Particularly, an abundance of Actinobacteria existed in Moechotypa diphysis and Mesosa hirsute, which eat broadleaf trees; however, no Actinobacteria were isolated from Corymbia rubra and Monochamus alternatus, which are needle-leaf eaters. Considerable proportions of xylanase and pectinase producing bacteria in the guts of the longicorn beetles implied that the bacteria may play an important role in the digestion of woody diets. Actinobacteria and Gammaproteobacteria were the dominant xylanase producers in the guts of the beetles.

Fast Mechanically Driven Daughter Cell Separation Is Widespread in Actinobacteria.

PubMed

Zhou, Xiaoxue; Halladin, David K; Theriot, Julie A

2016-08-30

Dividing cells of the coccoid Gram-positive bacterium Staphylococcus aureus undergo extremely rapid (millisecond) daughter cell separation (DCS) driven by mechanical crack propagation, a strategy that is very distinct from the gradual, enzymatically driven cell wall remodeling process that has been well described in several rod-shaped model bacteria. To determine if other bacteria, especially those in the same phylum (Firmicutes) or with similar coccoid shapes as S. aureus, might use a similar mechanically driven strategy for DCS, we used high-resolution video microscopy to examine cytokinesis in a phylogenetically wide range of species with various cell shapes and sizes. We found that fast mechanically driven DCS is rather rare in the Firmicutes (low G+C Gram positives), observed only in Staphylococcus and its closest coccoid relatives in the Macrococcus genus, and we did not observe this division strategy among the Gram-negative Proteobacteria In contrast, several members of the high-G+C Gram-positive phylum Actinobacteria (Micrococcus luteus, Brachybacterium faecium, Corynebacterium glutamicum, and Mycobacterium smegmatis) with diverse shapes ranging from coccoid to rod all undergo fast mechanical DCS during cell division. Most intriguingly, similar fast mechanical DCS was also observed during the sporulation of the actinobacterium Streptomyces venezuelae Much of our knowledge on bacterial cytokinesis comes from studying rod-shaped model organisms such as Escherichia coli and Bacillus subtilis Less is known about variations in this process among different bacterial species. While cell division in many bacteria has been characterized to some extent genetically or biochemically, few species have been examined using video microscopy to uncover the kinetics of cytokinesis and daughter cell separation (DCS). In this work, we found that fast (millisecond) DCS is exhibited by species in two independent clades of Gram-positive bacteria and is particularly prevalent

Optimizing the Electron Transfer Reactions at the Cathode of Microbial Fuel Cells

DTIC Science & Technology

2015-05-15

of iron-oxidizing Gram-negative eubacteria (Nitrospiraceae and Proteobacteria), Gram-positive eubacteria (Firmicutes and Actinobacteria ) and archaea...Euryarchaeota Actinobacteria Crenarachaeota Nitrospiraceae...Proteobacteria, Acidithiobacillus ferrooxidans; Firmicutes, Sulfobacillus thermosulfidooxidans; Actinobacteria , Ferrimicrobium acidiphilum; Euryarchaeota

Substrate-induced growth and isolation of Acidobacteria from acidic Sphagnum peat.

PubMed

Pankratov, Timofei A; Serkebaeva, Yulia M; Kulichevskaya, Irina S; Liesack, Werner; Dedysh, Svetlana N

2008-05-01

Fluorescence in situ hybridization (FISH) was applied to estimate the population size of the poorly characterized phylum Acidobacteria in acidic peat sampled from nine different Sphagnum-dominated wetlands of Northern Russia. The cell numbers of these bacteria in oxic peat layers ranged from 0.4 x 10(6) to 1.3 x 10(7) cells per g of wet peat, comprising up to 4% of total bacterial cells. Substrate-induced growth of acidobacteria was observed after amendment of peat samples with glucose, pectin, xylan, starch, ethanol and methanol, while weak or no response was obtained for acetate, pyruvate, mannitol and cellobiose. Using low-nutrient media and FISH-mediated monitoring of the isolation procedure, we succeeded in obtaining nine strains of acidobacteria in pure cultures. These strains belonged to subdivisions 1 and 3 of the Acidobacteria and represented strictly aerobic, heterotrophic organisms. Except for methanol, the substrate utilization patterns of these isolates matched the results obtained in our substrate-amendment experiments with native peat. All strains were also capable of utilizing galacturonic acid, a characteristic component of the cell wall in Sphagnum spp, which is released during moss decomposition. Most isolates from subdivision 1 were truly acidophilic organisms with the growth optimum at pH 3.5-4.5, while the isolates from subdivision 3 grew optimally at pH 5.5-6.5. Another important phenotypic trait of novel strains was their capability of active growth at low temperatures. Both acidophily and low-temperature growth are consistent with the occurrence of acidobacteria in cold and acidic northern wetlands.

Microbial Community Shifts Associated with RDX Loss in a Saturated and Well-Drained Surface Soil

DTIC Science & Technology

2005-03-01

community containing firmicutes (36%), proteobacteria (54%), actinobacteria (8%), and bacteroidetes (1%). The unsaturated soil contained a greater number of...genera (2.5 times that of the saturated soil) within similar phyla (19% firmicutes, 66% proteobacteria, 6% actinobacteria , 2% bacteroidetes, and 7...by the PLFA analysis. The T-RFLP analysis identified firmicutes (36%), proteobacteria (54%), actinobacteria (8%), and bacteroidetes (1%) in the

Community Composition of Bacterial Biofilms Formed on Simple Soil Based Bioelectrochemical Cell Anodes and Cathodes

DTIC Science & Technology

2012-04-01

included species of Actinobacteria ; however, only the anode biofilms produced species of Firmicutes and Proteobacteria. Analysis of TRFLP profiles...Molecular analyses, specifically of the 16S rRNA eubacterial gene, have also identified the presence of Firmicutes and Actinobacteria ERDC/CRREL TR...re- sulted in the identification of Firmicutes (typically Gram-positive) and Actinobacteria (often Gram-variable) on the anodes of fuel cells

Application of a new purification method of West-Kazakhstan chestnut soil microbiota DNA for metagenomic analysis

NASA Astrophysics Data System (ADS)

Sergaliev, N. Kh.; Kakishev, M. G.; Zhiengaliev, A. T.; Volodin, M. A.; Andronov, E. E.; Pinaev, A. G.

2015-04-01

A method for the extraction of soil microbial DNA has been tested on chestnut soils (Kastanozems) of the West Kazakhstan region. The taxonomic analysis of soil microbiome libraries has shown that the phyla Actinobacteria and Proteobacteria constitute the largest part of microbial communities in the analyzed soils. The Archaea form an appreciable part of the microbiome in the studied samples. In the underdeveloped dark chestnut soil, their portion is higher than 11%. This is of interest, as the proportion of Archaea in the soil communities of virgin lands usually does not exceed 5%. In addition to the phyla mentioned above, there are representatives of the phyla Acidobacteria, Bacteroidetes, Firmicutes, Gemmatimonadales, Planctomycetes, and Verrucomicrobia, which are all fairly common in soil communities.

A comparative analysis of microbiomes in natural and anthropogenically disturbed soils of northwestern Kazakhstan

NASA Astrophysics Data System (ADS)

Pershina, E. V.; Ivanova, E. A.; Nagieva, A. G.; Zhiengaliev, A. T.; Chirak, E. L.; Andronov, E. E.; Sergaliev, N. Kh.

2016-06-01

The goal of this study was to determine the relationships between the structure of the soil microbiome and the agroecological state of soils by the example of natural undisturbed (steppe areas) and anthropogenically disturbed (pastures, croplands, fallows) areas in the territory of northwestern Kazakhstan. The highest abundance of proteobacteria was found in the anthropogenically disturbed of fallows and in undisturbed soils; in other cases, actinobacteria and representatives of the Firmicutes phylum predominated. Different kinds of anthropogenic impacts resulted in the decrease in the portions of bacteria from the Acidobacteria, Gemmatimonadetes, and Firmicutes phyla. In the disturbed soils, the portions of bacteria from the Erysipelothrix, Mycobacterium, Methylibium, Skermanella, Ralstonia, Lactococcus, Bdellovibrio, Candidatus nitrososphaera, Catellatospora, Cellulomonas, Stenotrophomonas, and Steroidobacter genera increased. Bacteria of the Erysipelothrix and Methylibium genera occurred only in the undisturbed soils. The anthropogenically disturbed and undisturbed soils differed significantly in the taxonomic structure of their microbiomes forming two separate clusters, which confirms the efficiency of using the data on the structure of soil microbiomes when assessing the agroecological status of soils.

Differential Response of Acidobacteria Subgroups to Forest-to-Pasture Conversion and Their Biogeographic Patterns in the Western Brazilian Amazon

PubMed Central

Navarrete, Acacio A.; Venturini, Andressa M.; Meyer, Kyle M.; Klein, Ann M.; Tiedje, James M.; Bohannan, Brendan J. M.; Nüsslein, Klaus; Tsai, Siu M.; Rodrigues, Jorge L. M.

2015-01-01

Members of the phylum Acidobacteria are among the most abundant soil bacteria on Earth, but little is known about their response to environmental changes. We asked how the relative abundance and biogeographic patterning of this phylum and its subgroups responded to forest-to-pasture conversion in soils of the western Brazilian Amazon. Pyrosequencing of 16S rRNA genes was employed to assess the abundance and composition of the Acidobacteria community across 54 soil samples taken using a spatially nested sampling scheme at the landscape level. Numerically, Acidobacteria represented 20% of the total bacterial community in forest soils and 11% in pasture soils. Overall, 15 different Acidobacteria subgroups of the current 26 subgroups were detected, with Acidobacteria subgroups 1, 3, 5, and 6 accounting together for 87% of the total Acidobacteria community in forest soils and 75% in pasture soils. Concomitant with changes in soil chemistry after forest-to-pasture conversion—particularly an increase in properties linked to soil acidity and nutrient availability—we observed an increase in the relative abundances of Acidobacteria subgroups 4, 10, 17, and 18, and a decrease in the relative abundances of other Acidobacteria subgroups in pasture relative to forest soils. The composition of the total Acidobacteria community as well as the most abundant Acidobacteria subgroups (1, 3, 5, and 6) was significantly more similar in composition across space in pasture soils than in forest soils. These results suggest that preponderant responses of Acidobacteria subgroups, especially subgroups 1, 3, 4, 5, and 6, to forest-to-pasture conversion effects in soils could be used to define management-indicators of agricultural practices in the Amazon Basin. These acidobacterial responses are at least in part through alterations on acidity- and nutrient-related properties of the Amazon soils. PMID:26733981

Emerging biopharmaceuticals from marine actinobacteria.

PubMed

Hassan, Syed Shams Ul; Anjum, Komal; Abbas, Syed Qamar; Akhter, Najeeb; Shagufta, Bibi Ibtesam; Shah, Sayed Asmat Ali; Tasneem, Umber

2017-01-01

Actinobacteria are quotidian microorganisms in the marine world, playing a crucial ecological role in the recycling of refractory biomaterials and producing novel secondary metabolites with pharmaceutical applications. Actinobacteria have been isolated from the huge area of marine organisms including sponges, tunicates, corals, mollusks, crabs, mangroves and seaweeds. Natural products investigation of the marine actinobacteria revealed that they can synthesize numerous natural products including alkaloids, polyketides, peptides, isoprenoids, phenazines, sterols, and others. These natural products have a potential to provide future drugs against crucial diseases like cancer, HIV, microbial and protozoal infections and severe inflammations. Therefore, marine actinobacteria portray as a pivotal resource for marine drugs. It is an upcoming field of research to probe a novel and pharmaceutically important secondary metabolites from marine actinobacteria. In this review, we attempt to summarize the present knowledge on the diversity, chemistry and mechanism of action of marine actinobacteria-derived secondary metabolites from 2007 to 2016. Copyright © 2016 Elsevier B.V. All rights reserved.

Characterization of novel Acidobacteria exopolysaccharides with potential industrial and ecological applications

PubMed Central

Kielak, Anna M.; Castellane, Tereza C. L.; Campanharo, Joao C.; Colnago, Luiz A.; Costa, Ohana Y. A.; Corradi da Silva, Maria L.; van Veen, Johannes A.; Lemos, Eliana G. M.; Kuramae, Eiko E.

2017-01-01

Acidobacteria have been described as one of the most abundant and ubiquitous bacterial phyla in soil. However, factors contributing to this ecological success are not well elucidated mainly due to difficulties in bacterial isolation. Acidobacteria may be able to survive for long periods in soil due to protection provided by secreted extracellular polymeric substances that include exopolysaccharides (EPSs). Here we present the first study to characterize EPSs derived from two strains of Acidobacteria from subdivision 1 belonging to Granulicella sp. EPS are unique heteropolysaccharides containing mannose, glucose, galactose and xylose as major components, and are modified with carboxyl and methoxyl functional groups that we characterized by Fourier transform infrared (FTIR) spectroscopy. Both EPS compounds we identified can efficiently emulsify various oils (sunflower seed, diesel, and liquid paraffin) and hydrocarbons (toluene and hexane). Moreover, the emulsions are more thermostable over time than those of commercialized xanthan. Acidobacterial EPS can now be explored as a source of biopolymers that may be attractive and valuable for industrial applications due to their natural origin, sustainability, biodegradability and low toxicity. PMID:28117455

454 pyrosequencing analysis of bacterial diversity revealed by a comparative study of soils from mining subsidence and reclamation areas.

PubMed

Li, Yuanyuan; Chen, Longqian; Wen, Hongyu; Zhou, Tianjian; Zhang, Ting; Gao, Xiali

2014-03-28

Significant alteration in the microbial community can occur across reclamation areas suffering subsidence from mining. A reclamation site undergoing fertilization practices and an adjacent coal-excavated subsidence site (sites A and B, respectively) were examined to characterize the bacterial diversity using 454 high-throughput 16S rDNA sequencing. The dominant taxonomic groups in both the sites were Proteobacteria, Acidobacteria, Bacteroidetes, Betaproteobacteria, Actinobacteria, Gammaproteobacteria, Alphaproteobacteria, Deltaproteobacteria, Chloroflexi, and Firmicutes. However, the bacterial communities' abundance, diversity, and composition differed significantly between the sites. Site A presented higher bacterial diversity and more complex community structures than site B. The majority of sequences related to Proteobacteria, Gemmatimonadetes, Chloroflexi, Nitrospirae, Firmicutes, Betaproteobacteria, Deltaproteobacteria, and Anaerolineae were from site A; whereas those related to Actinobacteria, Planctomycetes, Bacteroidetes, Verrucomicrobia, Gammaproteobacteria, Nitriliruptoria, Alphaproteobacteria, and Phycisphaerae originated from site B. The distribution of some bacterial groups and subgroups in the two sites correlated with soil properties and vegetation due to reclamation practice. Site A exhibited enriched bacterial community, soil organic matter (SOM), and total nitrogen (TN), suggesting the presence of relatively diverse microorganisms. SOM and TN were important factors shaping the underlying microbial communities. Furthermore, the specific plant functional group (legumes) was also an important factor influencing soil microbial community composition. Thus, the effectiveness of 454 pyrosequencing in analyzing soil bacterial diversity was validated and an association between land ecological system restoration, mostly mediated by microbial communities, and an improvement in soil properties in coalmining reclamation areas was suggested.

Geomicrobiology of Nitrogen in a Coastal Aquifer: Isotopic and Molecular Methods to Examine Nitrification and Denitrification in Groundwater

DTIC Science & Technology

2010-06-01

respectively. Lesser 85 contributions were from the Actinobacteria -, Firmicute- and Planctomycetales-like organisms. The genes recovered from the gamma...the sediment core and represent potential denitrifying organisms in the nitrate-rich environment. Actinobacteria -like organisms are common soil...metabolites such as antibiotics (Bull and Stach 2007). Actinobacteria -like sequences were only recovered from the upper two meters. Firmicute-like

Long-term nitrogen fertilization decreases bacterial diversity and favors the growth of Actinobacteria and Proteobacteria in agro-ecosystems across the globe.

PubMed

Dai, Zhongmin; Su, Weiqin; Chen, Huaihai; Barberán, Albert; Zhao, Haochun; Yu, Mengjie; Yu, Lu; Brookes, Philip C; Schadt, Christopher W; Chang, Scott X; Xu, Jianming

2018-04-12

Long-term elevated nitrogen (N) input from anthropogenic sources may cause soil acidification and decrease crop yield, yet the response of the belowground microbial community to long-term N input alone or in combination with phosphorus (P) and potassium (K) is poorly understood. We explored the effect of long-term N and NPK fertilization on soil bacterial diversity and community composition using meta-analysis of a global dataset. Nitrogen fertilization decreased soil pH, and increased soil organic carbon (C) and available N contents. Bacterial taxonomic diversity was decreased by N fertilization alone, but was increased by NPK fertilization. The effect of N fertilization on bacterial diversity varied with soil texture and water management, but was independent of crop type or N application rate. Changes in bacterial diversity were positively related to both soil pH and organic C content under N fertilization alone, but only to soil organic C under NPK fertilization. Microbial biomass C decreased with decreasing bacterial diversity under long-term N fertilization. Nitrogen fertilization increased the relative abundance of Proteobacteria and Actinobacteria, but reduced the abundance of Acidobacteria, consistent with the general life history strategy theory for bacteria. The positive correlation between N application rate and the relative abundance of Actinobacteria indicates that increased N availability favored the growth of Actinobacteria. This first global analysis of long-term N and NPK fertilization that differentially affects bacterial diversity and community composition provides a reference for nutrient management strategies for maintaining belowground microbial diversity in agro-ecosystems worldwide. © 2018 John Wiley & Sons Ltd.

Veillonella, Firmicutes: Microbes disguised as Gram negatives.

PubMed

Vesth, Tammi; Ozen, Aslı; Andersen, Sandra C; Kaas, Rolf Sommer; Lukjancenko, Oksana; Bohlin, Jon; Nookaew, Intawat; Wassenaar, Trudy M; Ussery, David W

2013-12-20

The Firmicutes represent a major component of the intestinal microflora. The intestinal Firmicutes are a large, diverse group of organisms, many of which are poorly characterized due to their anaerobic growth requirements. Although most Firmicutes are Gram positive, members of the class Negativicutes, including the genus Veillonella, stain Gram negative. Veillonella are among the most abundant organisms of the oral and intestinal microflora of animals and humans, in spite of being strict anaerobes. In this work, the genomes of 24 Negativicutes, including eight Veillonella spp., are compared to 20 other Firmicutes genomes; a further 101 prokaryotic genomes were included, covering 26 phyla. Thus a total of 145 prokaryotic genomes were analyzed by various methods to investigate the apparent conflict of the Veillonella Gram stain and their taxonomic position within the Firmicutes. Comparison of the genome sequences confirms that the Negativicutes are distantly related to Clostridium spp., based on 16S rRNA, complete genomic DNA sequences, and a consensus tree based on conserved proteins. The genus Veillonella is relatively homogeneous: inter-genus pair-wise comparison identifies at least 1,350 shared proteins, although less than half of these are found in any given Clostridium genome. Only 27 proteins are found conserved in all analyzed prokaryote genomes. Veillonella has distinct metabolic properties, and significant similarities to genomes of Proteobacteria are not detected, with the exception of a shared LPS biosynthesis pathway. The clade within the class Negativicutes to which the genus Veillonella belongs exhibits unique properties, most of which are in common with Gram-positives and some with Gram negatives. They are only distantly related to Clostridia, but are even less closely related to Gram-negative species. Though the Negativicutes stain Gram-negative and possess two membranes, the genome and proteome analysis presented here confirm their place within the

Veillonella, Firmicutes: Microbes disguised as Gram negatives

PubMed Central

Vesth, Tammi; Ozen, Aslı; Andersen, Sandra C.; Kaas, Rolf Sommer; Lukjancenko, Oksana; Bohlin, Jon; Nookaew, Intawat; Wassenaar, Trudy M.; Ussery, David W.

2013-01-01

The Firmicutes represent a major component of the intestinal microflora. The intestinal Firmicutes are a large, diverse group of organisms, many of which are poorly characterized due to their anaerobic growth requirements. Although most Firmicutes are Gram positive, members of the class Negativicutes, including the genus Veillonella, stain Gram negative. Veillonella are among the most abundant organisms of the oral and intestinal microflora of animals and humans, in spite of being strict anaerobes. In this work, the genomes of 24 Negativicutes, including eight Veillonella spp., are compared to 20 other Firmicutes genomes; a further 101 prokaryotic genomes were included, covering 26 phyla. Thus a total of 145 prokaryotic genomes were analyzed by various methods to investigate the apparent conflict of the Veillonella Gram stain and their taxonomic position within the Firmicutes. Comparison of the genome sequences confirms that the Negativicutes are distantly related to Clostridium spp., based on 16S rRNA, complete genomic DNA sequences, and a consensus tree based on conserved proteins. The genus Veillonella is relatively homogeneous: inter-genus pair-wise comparison identifies at least 1,350 shared proteins, although less than half of these are found in any given Clostridium genome. Only 27 proteins are found conserved in all analyzed prokaryote genomes. Veillonella has distinct metabolic properties, and significant similarities to genomes of Proteobacteria are not detected, with the exception of a shared LPS biosynthesis pathway. The clade within the class Negativicutes to which the genus Veillonella belongs exhibits unique properties, most of which are in common with Gram-positives and some with Gram negatives. They are only distantly related to Clostridia, but are even less closely related to Gram-negative species. Though the Negativicutes stain Gram-negative and possess two membranes, the genome and proteome analysis presented here confirm their place within the

Development of Biomarkers for Assessing In Situ RDX Biodegradation Potential

DTIC Science & Technology

2010-02-01

within the Ribosomal Database Project (Michigan State University), belonged to Actinobacteria , Acidobacteria, α-Proteobacteria, γ-Proteobacteria, δ...These included bacteria belonging to Actinobacteria (two clones), α- Proteobacteria (seven clones), and γ-Proteobacteria (six clones). The authors

Molecular-based environmental risk assessment of three varieties of genetically engineered cows.

PubMed

Xu, Jianxiang; Zhao, Jie; Wang, Jianwu; Zhao, Yaofeng; Zhang, Lei; Chu, Mingxing; Li, Ning

2011-10-01

The development of animal biotechnology has led to an increase in attention to biosafety issues. Here we evaluated the impact of genetically engineered cows on the environment. The probability of horizontal gene transfer and the impact on the microbial communities in cow gut and soil were tested using three varieties of genetically engineered cows that were previously transformed with a human gene encoding lysozyme, lactoferrin, or human alpha lactalbumin. The results showed that the transgenes were not detectable by polymerase chain reaction (PCR) or quantitative real-time PCR in gut microbial DNA extracts of manure or microbial DNA extracts of topsoil. In addition, the transgenes had no impact on the microbial communities in cow gut or soil as assessed by PCR-denaturing gradient gel electrophoresis or 16S rDNA sequencing. Furthermore, phylogenetic analyses showed that the manure bacteria sampled during each of the four seasons belonged primarily to two groups, Firmicutes and Bacteroidetes, and the soil bacteria belonged to four groups, Firmicutes, Bacteroidetes, Actinobacteria, and α-proteobacteria. Other groups, such as β-proteobacteria, γ-proteobacteria, δ-proteobacteria, ε-proteobacteria, Spirochaetes, Acidobacteria, Chloroflexi, and Nitrospira, were not dominant in the manure or soil.

Structure of the human gastric bacterial community in relation to Helicobacter pylori status.

PubMed

Maldonado-Contreras, Ana; Goldfarb, Kate C; Godoy-Vitorino, Filipa; Karaoz, Ulas; Contreras, Mónica; Blaser, Martin J; Brodie, Eoin L; Dominguez-Bello, Maria G

2011-04-01

The human stomach is naturally colonized by Helicobacter pylori, which, when present, dominates the gastric bacterial community. In this study, we aimed to characterize the structure of the bacterial community in the stomach of patients of differing H. pylori status. We used a high-density 16S rRNA gene microarray (PhyloChip, Affymetrix, Inc.) to hybridize 16S rRNA gene amplicons from gastric biopsy DNA of 10 rural Amerindian patients from Amazonas, Venezuela, and of two immigrants to the United States (from South Asia and Africa, respectively). H. pylori status was determined by PCR amplification of H. pylori glmM from gastric biopsy samples. Of the 12 patients, 8 (6 of the 10 Amerindians and the 2 non-Amerindians) were H. pylori glmM positive. Regardless of H. pylori status, the PhyloChip detected Helicobacteriaceae DNA in all patients, although with lower relative abundance in patients who were glmM negative. The G2-chip taxonomy analysis of PhyloChip data indicated the presence of 44 bacterial phyla (of which 16 are unclassified by the Taxonomic Outline of the Bacteria and Archaea taxonomy) in a highly uneven community dominated by only four phyla: Proteobacteria, Firmicutes, Actinobacteria and Bacteroidetes. Positive H. pylori status was associated with increased relative abundance of non-Helicobacter bacteria from the Proteobacteria, Spirochetes and Acidobacteria, and with decreased abundance of Actinobacteria, Bacteroidetes and Firmicutes. The PhyloChip detected richness of low abundance phyla, and showed marked differences in the structure of the gastric bacterial community according to H. pylori status.

Structure of the human gastric bacterial community in relation to Helicobacter pylori status

PubMed Central

Maldonado-Contreras, Ana; Goldfarb, Kate C; Godoy-Vitorino, Filipa; Karaoz, Ulas; Contreras, Mónica; Blaser, Martin J; Brodie, Eoin L; Dominguez-Bello, Maria G

2011-01-01

The human stomach is naturally colonized by Helicobacter pylori, which, when present, dominates the gastric bacterial community. In this study, we aimed to characterize the structure of the bacterial community in the stomach of patients of differing H. pylori status. We used a high-density 16S rRNA gene microarray (PhyloChip, Affymetrix, Inc.) to hybridize 16S rRNA gene amplicons from gastric biopsy DNA of 10 rural Amerindian patients from Amazonas, Venezuela, and of two immigrants to the United States (from South Asia and Africa, respectively). H. pylori status was determined by PCR amplification of H. pylori glmM from gastric biopsy samples. Of the 12 patients, 8 (6 of the 10 Amerindians and the 2 non-Amerindians) were H. pylori glmM positive. Regardless of H. pylori status, the PhyloChip detected Helicobacteriaceae DNA in all patients, although with lower relative abundance in patients who were glmM negative. The G2-chip taxonomy analysis of PhyloChip data indicated the presence of 44 bacterial phyla (of which 16 are unclassified by the Taxonomic Outline of the Bacteria and Archaea taxonomy) in a highly uneven community dominated by only four phyla: Proteobacteria, Firmicutes, Actinobacteria and Bacteroidetes. Positive H. pylori status was associated with increased relative abundance of non-Helicobacter bacteria from the Proteobacteria, Spirochetes and Acidobacteria, and with decreased abundance of Actinobacteria, Bacteroidetes and Firmicutes. The PhyloChip detected richness of low abundance phyla, and showed marked differences in the structure of the gastric bacterial community according to H. pylori status. PMID:20927139

Genomic Analysis of Complex Microbial Communities in Wounds

DTIC Science & Technology

2009-07-01

Actinobacteria — were the most commonly misclassified [25]. The 16S sequences used in the current study were all greater than or equal to 200 bases...with most (89.1%) of the sequences falling into Firmicutes, Proteobac- teria, and Actinobacteria phyla. High percentages of the Firmicutes and... Actinobacteria sequences were successfully assigned to the genus level, 88.0% and 82.3%, respectively; however, only 53.0% of the Proteobacteria sequences

Comparative analyses of the bacterial microbiota of the human nostril and oropharynx.

PubMed

Lemon, Katherine P; Klepac-Ceraj, Vanja; Schiffer, Hilary K; Brodie, Eoin L; Lynch, Susan V; Kolter, Roberto

2010-06-22

The nose and throat are important sites of pathogen colonization, yet the microbiota of both is relatively unexplored by culture-independent approaches. We examined the bacterial microbiota of the nostril and posterior wall of the oropharynx from seven healthy adults using two culture-independent methods, a 16S rRNA gene microarray (PhyloChip) and 16S rRNA gene clone libraries. While the bacterial microbiota of the oropharynx was richer than that of the nostril, the oropharyngeal microbiota varied less among participants than did nostril microbiota. A few phyla accounted for the majority of the bacteria detected at each site: Firmicutes and Actinobacteria in the nostril and Firmicutes, Proteobacteria, and Bacteroidetes in the oropharynx. Compared to culture-independent surveys of microbiota from other body sites, the microbiota of the nostril and oropharynx show distinct phylum-level distribution patterns, supporting niche-specific colonization at discrete anatomical sites. In the nostril, the distribution of Actinobacteria and Firmicutes was reminiscent of that of skin, though Proteobacteria were much less prevalent. The distribution of Firmicutes, Proteobacteria, and Bacteroidetes in the oropharynx was most similar to that in saliva, with more Proteobacteria than in the distal esophagus or mouth. While Firmicutes were prevalent at both sites, distinct families within this phylum dominated numerically in each. At both sites there was an inverse correlation between the prevalences of Firmicutes and another phylum: in the oropharynx, Firmicutes and Proteobacteria, and in the nostril, Firmicutes and Actinobacteria. In the nostril, this inverse correlation existed between the Firmicutes family Staphylococcaceae and Actinobacteria families, suggesting potential antagonism between these groups.

Recent advances in genetic modification systems for Actinobacteria.

PubMed

Deng, Yu; Zhang, Xi; Zhang, Xiaojuan

2017-03-01

Actinobacteria are extremely important to human health, agriculture, and forests. Because of the vast differences of the characteristics of Actinobacteria, a lot of genetic tools have been developed for efficiently manipulating the genetics. Although there are a lot of successful examples of engineering Actinobacteria, they are still more difficult to be genetically manipulated than other model microorganisms such as Saccharomyces cerevisiae, Escherichia coli, and Bacillus subtilis etc. due to the diverse genomics and biochemical machinery. Here, we review the methods to introduce heterologous DNA into Actinobacteria and the available genetic modification tools. The trends and problems existing in engineering Actinobacteria are also covered.

Metagenomic analysis of microbial consortia enriched from compost: new insights into the role of Actinobacteria in lignocellulose decomposition.

PubMed

Wang, Cheng; Dong, Da; Wang, Haoshu; Müller, Karin; Qin, Yong; Wang, Hailong; Wu, Weixiang

2016-01-01

Compost habitats sustain a vast ensemble of microbes specializing in the degradation of lignocellulosic plant materials and are thus important both for their roles in the global carbon cycle and as potential sources of biochemical catalysts for advanced biofuels production. Studies have revealed substantial diversity in compost microbiomes, yet how this diversity relates to functions and even to the genes encoding lignocellulolytic enzymes remains obscure. Here, we used a metagenomic analysis of the rice straw-adapted (RSA) microbial consortia enriched from compost ecosystems to decipher the systematic and functional contexts within such a distinctive microbiome. Analyses of the 16S pyrotag library and 5 Gbp of metagenomic sequence showed that the phylum Actinobacteria was the predominant group among the Bacteria in the RSA consortia, followed by Proteobacteria, Firmicutes, Chloroflexi, and Bacteroidetes. The CAZymes profile revealed that CAZyme genes in the RSA consortia were also widely distributed within these bacterial phyla. Strikingly, about 46.1 % of CAZyme genes were from actinomycetal communities, which harbored a substantially expanded catalog of the cellobiohydrolase, β-glucosidase, acetyl xylan esterase, arabinofuranosidase, pectin lyase, and ligninase genes. Among these communities, a variety of previously unrecognized species was found, which reveals a greater ecological functional diversity of thermophilic Actinobacteria than previously assumed. These data underline the pivotal role of thermophilic Actinobacteria in lignocellulose biodegradation processes in the compost habitat. Besides revealing a new benchmark for microbial enzymatic deconstruction of lignocelluloses, the results suggest that actinomycetes found in compost ecosystems are potential candidates for mining efficient lignocellulosic enzymes in the biofuel industry.

Effect of the natural arsenic gradient on the diversity and arsenic resistance of bacterial communities of the sediments of Camarones River (Atacama Desert, Chile).

PubMed

Leon, Carla G; Moraga, Ruben; Valenzuela, Cristian; Gugliandolo, Concetta; Lo Giudice, Angelina; Papale, Maria; Vilo, Claudia; Dong, Qunfeng; Smith, Carlos T; Rossello-Mora, Ramon; Yañez, Jorge; Campos, Victor L

2018-01-01

Arsenic (As), a highly toxic metalloid, naturally present in Camarones River (Atacama Desert, Chile) is a great health concern for the local population and authorities. In this study, the taxonomic and functional characterization of bacterial communities associated to metal-rich sediments from three sites of the river (sites M1, M2 and M3), showing different arsenic concentrations, were evaluated using a combination of approaches. Diversity of bacterial communities was evaluated by Illumina sequencing. Strains resistant to arsenic concentrations varying from 0.5 to 100 mM arsenite or arsenate were isolated and the presence of genes coding for enzymes involved in arsenic oxidation (aio) or reduction (arsC) investigated. Bacterial communities showed a moderate diversity which increased as arsenic concentrations decreased along the river. Sequences of the dominant taxonomic groups (abundances ≥1%) present in all three sites were affiliated to Proteobacteria (range 40.3-47.2%), Firmicutes (8.4-24.8%), Acidobacteria (10.4-17.1%), Actinobacteria (5.4-8.1%), Chloroflexi (3.9-7.5%), Planctomycetes (1.2-5.3%), Gemmatimonadetes (1.2-1.5%), and Nitrospirae (1.1-1.2%). Bacterial communities from sites M2 and M3 showed no significant differences in diversity between each other (p = 0.9753) but they were significantly more diverse than M1 (p<0.001 and p<0.001, respectively). Sequences affiliated with Proteobacteria, Firmicutes, Acidobacteria, Chloroflexi and Actinobacteria at M1 accounted for more than 89% of the total classified bacterial sequences present but these phyla were present in lesser proportions in M2 and M3 sites. Strains isolated from the sediment of sample M1, having the greatest arsenic concentration (498 mg kg-1), showed the largest percentages of arsenic oxidation and reduction. Genes aio were more frequently detected in isolates from M1 (54%), whereas arsC genes were present in almost all isolates from all three sediments, suggesting that bacterial

Effect of the natural arsenic gradient on the diversity and arsenic resistance of bacterial communities of the sediments of Camarones River (Atacama Desert, Chile)

PubMed Central

Leon, Carla G.; Moraga, Ruben; Valenzuela, Cristian; Gugliandolo, Concetta; Lo Giudice, Angelina; Papale, Maria; Vilo, Claudia; Dong, Qunfeng; Smith, Carlos T.; Rossello-Mora, Ramon; Yañez, Jorge

2018-01-01

Arsenic (As), a highly toxic metalloid, naturally present in Camarones River (Atacama Desert, Chile) is a great health concern for the local population and authorities. In this study, the taxonomic and functional characterization of bacterial communities associated to metal-rich sediments from three sites of the river (sites M1, M2 and M3), showing different arsenic concentrations, were evaluated using a combination of approaches. Diversity of bacterial communities was evaluated by Illumina sequencing. Strains resistant to arsenic concentrations varying from 0.5 to 100 mM arsenite or arsenate were isolated and the presence of genes coding for enzymes involved in arsenic oxidation (aio) or reduction (arsC) investigated. Bacterial communities showed a moderate diversity which increased as arsenic concentrations decreased along the river. Sequences of the dominant taxonomic groups (abundances ≥1%) present in all three sites were affiliated to Proteobacteria (range 40.3–47.2%), Firmicutes (8.4–24.8%), Acidobacteria (10.4–17.1%), Actinobacteria (5.4–8.1%), Chloroflexi (3.9–7.5%), Planctomycetes (1.2–5.3%), Gemmatimonadetes (1.2–1.5%), and Nitrospirae (1.1–1.2%). Bacterial communities from sites M2 and M3 showed no significant differences in diversity between each other (p = 0.9753) but they were significantly more diverse than M1 (p<0.001 and p<0.001, respectively). Sequences affiliated with Proteobacteria, Firmicutes, Acidobacteria, Chloroflexi and Actinobacteria at M1 accounted for more than 89% of the total classified bacterial sequences present but these phyla were present in lesser proportions in M2 and M3 sites. Strains isolated from the sediment of sample M1, having the greatest arsenic concentration (498 mg kg-1), showed the largest percentages of arsenic oxidation and reduction. Genes aio were more frequently detected in isolates from M1 (54%), whereas arsC genes were present in almost all isolates from all three sediments, suggesting that

Under-detection of endospore-forming Firmicutes in metagenomic data

DOE PAGES

Filippidou, Sevasti; Junier, Thomas; Wunderlin, Tina; ...

2015-04-25

Microbial diversity studies based on metagenomic sequencing have greatly enhanced our knowledge of the microbial world. However, one caveat is the fact that not all microorganisms are equally well detected, questioning the universality of this approach. Firmicutes are known to be a dominant bacterial group. Several Firmicutes species are endospore formers and this property makes them hardy in potentially harsh conditions, and thus likely to be present in a wide variety of environments, even as residents and not functional players. While metagenomic libraries can be expected to contain endospore formers, endospores are known to be resilient to many traditional methodsmore » of DNA isolation and thus potentially undetectable. In this study we evaluated the representation of endospore-forming Firmicutes in 73 published metagenomic datasets using two molecular markers unique to this bacterial group ( spo0A and gpr). Both markers were notably absent in well-known habitats of Firmicutes such as soil, with spo0A found only in three mammalian gut microbiomes. A tailored DNA extraction method resulted in the detection of a large diversity of endospore-formers in amplicon sequencing of the 16S rRNA and spo0A genes. However, shotgun classification was still poor with only a minor fraction of the community assigned to Firmicutes. Thus, removing a specific bias in a molecular workflow improves detection in amplicon sequencing, but it was insufficient to overcome the limitations for detecting endospore-forming Firmicutes in whole-genome metagenomics. In conclusion, this study highlights the importance of understanding the specific methodological biases that can contribute to improve the universality of metagenomic approaches.« less

Under-detection of endospore-forming Firmicutes in metagenomic data

DOE Office of Scientific and Technical Information (OSTI.GOV)

Filippidou, Sevasti; Junier, Thomas; Wunderlin, Tina

Microbial diversity studies based on metagenomic sequencing have greatly enhanced our knowledge of the microbial world. However, one caveat is the fact that not all microorganisms are equally well detected, questioning the universality of this approach. Firmicutes are known to be a dominant bacterial group. Several Firmicutes species are endospore formers and this property makes them hardy in potentially harsh conditions, and thus likely to be present in a wide variety of environments, even as residents and not functional players. While metagenomic libraries can be expected to contain endospore formers, endospores are known to be resilient to many traditional methodsmore » of DNA isolation and thus potentially undetectable. In this study we evaluated the representation of endospore-forming Firmicutes in 73 published metagenomic datasets using two molecular markers unique to this bacterial group ( spo0A and gpr). Both markers were notably absent in well-known habitats of Firmicutes such as soil, with spo0A found only in three mammalian gut microbiomes. A tailored DNA extraction method resulted in the detection of a large diversity of endospore-formers in amplicon sequencing of the 16S rRNA and spo0A genes. However, shotgun classification was still poor with only a minor fraction of the community assigned to Firmicutes. Thus, removing a specific bias in a molecular workflow improves detection in amplicon sequencing, but it was insufficient to overcome the limitations for detecting endospore-forming Firmicutes in whole-genome metagenomics. In conclusion, this study highlights the importance of understanding the specific methodological biases that can contribute to improve the universality of metagenomic approaches.« less

Apatite and Chitin Amendments Promote Microbial Activity and Augment Metal Removal in Marine Sediments

DTIC Science & Technology

2013-07-01

abundance of Deltaproteobacteria and decrease of Actinobacteria , Alphaproteobacteria, and Nitrospirae. Many of these groups of bacteria have been shown to...shifts were observed from clone library analyses (Table 2 and Fig- ure 4). Actinobacteria , Alphaproteobacteria, Gam- maproteobacteria...abundance (%) Phylum FUS FCS FACS Impact Acidobacteria - - 1.9 Induced Actinobacteria 20.8 8.6 3.8 Decreased Alphaproteobacteria 22.9 14.3 13.2 Decreased

Genomic insights into the Acidobacteria reveal strategies for their success in terrestrial environments

PubMed Central

Trojan, Daniela; Roux, Simon; Herbold, Craig; Rattei, Thomas; Woebken, Dagmar

2018-01-01

Summary Members of the phylum Acidobacteria are abundant and ubiquitous across soils. We performed a large‐scale comparative genome analysis spanning subdivisions 1, 3, 4, 6, 8 and 23 (n = 24) with the goal to identify features to help explain their prevalence in soils and understand their ecophysiology. Our analysis revealed that bacteriophage integration events along with transposable and mobile elements influenced the structure and plasticity of these genomes. Low‐ and high‐affinity respiratory oxygen reductases were detected in multiple genomes, suggesting the capacity for growing across different oxygen gradients. Among many genomes, the capacity to use a diverse collection of carbohydrates, as well as inorganic and organic nitrogen sources (such as via extracellular peptidases), was detected – both advantageous traits in environments with fluctuating nutrient environments. We also identified multiple soil acidobacteria with the potential to scavenge atmospheric concentrations of H2, now encompassing mesophilic soil strains within the subdivision 1 and 3, in addition to a previously identified thermophilic strain in subdivision 4. This large‐scale acidobacteria genome analysis reveal traits that provide genomic, physiological and metabolic versatility, presumably allowing flexibility and versatility in the challenging and fluctuating soil environment. PMID:29327410

Enrichment of Desulfitobacterium spp. from forest and grassland soil using the O-demethylation of phenyl methyl ethers as a growth-selective process.

PubMed

Mingo, Felix Sebastian; Diekert, Gabriele; Studenik, Sandra

2016-02-01

The O-demethylation of phenyl methyl ethers under anaerobic conditions is a metabolic feature of acetogens and Desulfitobacterium spp. Desulfitobacteria as well as most acetogens are Gram-positive bacteria with a low GC content and belong to the phylum Firmicutes. The consumption of the phenyl methyl ether syringate was studied in enrichment cultures originating from five different topsoils. Desulfitobacterium spp. were detected in all topsoils via quantitative PCR. Desulfitobacteria could be enriched using the O-demethylation of syringate as a growth-selective process. The enrichment was significantly favoured by an external electron acceptor such as 3-chloro-4-hydroxyphenylacetate or thiosulfate. Upon cultivation in the presence of syringate and thiosulfate, which naturally occur in soil, a maximum number of 16S rRNA gene copies of Desulfitobacterium spp. was reached within the first three subcultivation steps and accounted for 3-10% of the total microbial community depending on the soil type. Afterwards, a loss of Desulfitobacterium gene copies was observed. Community analyses revealed that Proteobacteria, Acidobacteria, Actinobacteria and Bacteroidetes were the main phyla in the initial soil samples. Upon addition of syringate and thiosulfate as growth substrates, these phyla were rapidly outcompeted by Firmicutes, which were under-represented in soil. The main Firmicutes genera identified were Alkalibaculum, Clostridium, Sporobacterium, Sporomusa and Tissierella, which might be responsible for outcompeting the desulfitobacteria. Most of these organisms belong to the acetogens, which have previously been described to demethylate phenyl methyl ethers. The shift of the native community structure to almost exclusively Firmicutes supports the participation of members of this phylum in environmental demethylation processes.

Production of Enzymes from Marine Actinobacteria.

PubMed

Zhao, X Q; Xu, X N; Chen, L Y

Marine actinobacteria are well recognized for their capabilities to produce valuable natural products, which have great potential for applications in medical, agricultural, and fine chemical industries. In addition to producing unique enzymes responsible for biosynthesis of natural products, many marine actinobacteria also produce hydrolytic enzymes which are able to degrade various biopolymers, such as cellulose, xylan, and chitin. These enzymes are important to produce biofuels and biochemicals of interest from renewable biomass. In this chapter, the recent reports of novel enzymes produced by marine actinobacteria are reviewed, and advanced technologies that can be applied to search for novel marine enzymes as well as for improved enzyme production by marine actinobacteria are summarized, which include ribosome engineering, genome mining, as well as synthetic biology studies. © 2016 Elsevier Inc. All rights reserved.

Pharmaceutically active secondary metabolites of marine actinobacteria.

PubMed

Manivasagan, Panchanathan; Venkatesan, Jayachandran; Sivakumar, Kannan; Kim, Se-Kwon

2014-04-01

Marine actinobacteria are one of the most efficient groups of secondary metabolite producers and are very important from an industrial point of view. Many representatives of the order Actinomycetales are prolific producers of thousands of biologically active secondary metabolites. Actinobacteria from terrestrial sources have been studied and screened since the 1950s, for many important antibiotics, anticancer, antitumor and immunosuppressive agents. However, frequent rediscovery of the same compounds from the terrestrial actinobacteria has made them less attractive for screening programs in the recent years. At the same time, actinobacteria isolated from the marine environment have currently received considerable attention due to the structural diversity and unique biological activities of their secondary metabolites. They are efficient producers of new secondary metabolites that show a range of biological activities including antibacterial, antifungal, anticancer, antitumor, cytotoxic, cytostatic, anti-inflammatory, anti-parasitic, anti-malaria, antiviral, antioxidant, anti-angiogenesis, etc. In this review, an evaluation is made on the current status of research on marine actinobacteria yielding pharmaceutically active secondary metabolites. Bioactive compounds from marine actinobacteria possess distinct chemical structures that may form the basis for synthesis of new drugs that could be used to combat resistant pathogens. With the increasing advancement in science and technology, there would be a greater demand for new bioactive compounds synthesized by actinobacteria from various marine sources in future. Copyright © 2013 Elsevier GmbH. All rights reserved.

Variability of Actinobacteria, a minor component of rumen microflora.

PubMed

Suľák, M; Sikorová, L; Jankuvová, J; Javorský, P; Pristaš, P

2012-07-01

Actinobacteria (Actinomycetes) are a significant and interesting group of gram-positive bacteria. They are regular, though infrequent, members of the microbial life in the rumen and represent up to 3 % of total rumen bacteria; there is considerable lack of information about ecology and biology of rumen actinobacteria. During the characterization of variability of rumen treponemas using non-cultivation approach, we also noted the variability of rumen actinobacteria. By using Treponema-specific primers a specific 16S rRNA gene library was prepared from cow and sheep rumen total DNA. About 10 % of recombinant clones contained actinobacteria-like sequences. Phylogenetic analyses of 11 clones obtained showed the high variability of actinobacteria in the ruminant digestive system. While some sequences are nearly identical to known sequences of actinobacteria, we detected completely new clusters of actinobacteria-like sequences, representing probably new, as yet undiscovered, group of rumen Actinobacteria. Further research will be necessary for understanding their nature and functions in the rumen.

The community distribution of bacteria and fungi on ancient wall paintings of the Mogao Grottoes

PubMed Central

Ma, Yantian; Zhang, He; Du, Ye; Tian, Tian; Xiang, Ting; Liu, Xiande; Wu, Fasi; An, Lizhe; Wang, Wanfu; Gu, Ji-Dong; Feng, Huyuan

2015-01-01

In this study, we compared the microbial communities colonising ancient cave wall paintings of the Mogao Grottoes exhibiting signs of biodeterioration. Ten samples were collected from five different caves built during different time periods and analysed using culture-independent and culture-dependent methods. The clone library results revealed high microbial diversity, including the bacterial groups Firmicutes, Proteobacteria, Actinobacteria, Acidobacteria, Cyanobacteria, Bacteroidetes, Gemmatimonadetes, Planctomycetes, and Chloroflexi and the fungal groups Euascomycetes, Dothideomycetes, Eurotiomycetes, Sordariomycetes, Saccharomycetes, Plectomycetes, Pezizomycetes, Zygomycota, and Basidiomycota. The bacterial community structures differed among the samples, with no consistent temporal or spatial trends. However, the fungal community diversity index correlated with the building time of the caves independent of environmental factors (e.g., temperature or relative humidity). The enrichment cultures revealed that many culturable strains were highly resistant to various stresses and thus may be responsible for the damage to cave paintings in the Mogao Grottoes. PMID:25583346

The community distribution of bacteria and fungi on ancient wall paintings of the Mogao Grottoes.

PubMed

Ma, Yantian; Zhang, He; Du, Ye; Tian, Tian; Xiang, Ting; Liu, Xiande; Wu, Fasi; An, Lizhe; Wang, Wanfu; Gu, Ji-Dong; Feng, Huyuan

2015-01-13

In this study, we compared the microbial communities colonising ancient cave wall paintings of the Mogao Grottoes exhibiting signs of biodeterioration. Ten samples were collected from five different caves built during different time periods and analysed using culture-independent and culture-dependent methods. The clone library results revealed high microbial diversity, including the bacterial groups Firmicutes, Proteobacteria, Actinobacteria, Acidobacteria, Cyanobacteria, Bacteroidetes, Gemmatimonadetes, Planctomycetes, and Chloroflexi and the fungal groups Euascomycetes, Dothideomycetes, Eurotiomycetes, Sordariomycetes, Saccharomycetes, Plectomycetes, Pezizomycetes, Zygomycota, and Basidiomycota. The bacterial community structures differed among the samples, with no consistent temporal or spatial trends. However, the fungal community diversity index correlated with the building time of the caves independent of environmental factors (e.g., temperature or relative humidity). The enrichment cultures revealed that many culturable strains were highly resistant to various stresses and thus may be responsible for the damage to cave paintings in the Mogao Grottoes.

Ether- and Ester-Bound iso-Diabolic Acid and Other Lipids in Members of Acidobacteria Subdivision 4

PubMed Central

Rijpstra, W. Irene C.; Hopmans, Ellen C.; Foesel, Bärbel U.; Wüst, Pia K.; Overmann, Jörg; Tank, Marcus; Bryant, Donald A.; Dunfield, Peter F.; Houghton, Karen; Stott, Matthew B.

2014-01-01

Recently, iso-diabolic acid (13,16-dimethyl octacosanedioic acid) has been identified as a major membrane-spanning lipid of subdivisions 1 and 3 of the Acidobacteria, a highly diverse phylum within the Bacteria. This finding pointed to the Acidobacteria as a potential source for the bacterial glycerol dialkyl glycerol tetraethers that occur ubiquitously in peat, soil, lakes, and hot springs. Here, we examined the lipid composition of seven phylogenetically divergent strains of subdivision 4 of the Acidobacteria, a bacterial group that is commonly encountered in soil. Acid hydrolysis of total cell material released iso-diabolic acid derivatives in substantial quantities (11 to 48% of all fatty acids). In contrast to subdivisions 1 and 3 of the Acidobacteria, 6 out of the 7 species of subdivision 4 (excepting “Candidatus Chloracidobacterium thermophilum”) contained iso-diabolic acid ether bound to a glycerol in larger fractional abundance than iso-diabolic acid itself. This is in agreement with the analysis of intact polar lipids (IPLs) by high-performance liquid chromatography-mass spectrometry (HPLC-MS), which showed the dominance of mixed ether-ester glycerides. iso-Diabolic acid-containing IPLs were not identified, because these IPLs are not released with a Bligh-Dyer extraction, as observed before when studying lipid compositions of subdivisions 1 and 3 of the Acidobacteria. The presence of ether bonds in the membrane lipids does not seem to be an adaptation to temperature, because the five mesophilic isolates contained a larger amount of ether lipids than the thermophile “Ca. Chloracidobacterium thermophilum.” Furthermore, experiments with Pyrinomonas methylaliphatogenes did not reveal a major influence of growth temperature over the 50 to 69°C range. PMID:24928878

Long-term nitrogen fertilization decreases bacterial diversity and favors the growth of Actinobacteria and Proteobacteria in agro-ecosystems across the globe

DOE Office of Scientific and Technical Information (OSTI.GOV)

Dai, Zhongmin; Su, Weiqin; Chen, Huaihai

Long-term Elevated nitrogen (N) input from anthropogenic sources may cause soil acidification and decrease crop yield, yet the response of the belowground microbial community to long-term N input and the input of N combined with phosphorus (P) and potassium (K) is still poorly understood. Here, we explored the effect of long-term N and NPK fertilization on soil bacterial diversity and community composition using meta-analysis of a global dataset. Nitrogen fertilization decreased soil pH, and increased soil organic carbon (C) and available N contents. Bacterial taxonomic diversity was decreased by N fertilization alone, but was increased by NPK fertilization. The effectmore » of N fertilization on bacterial diversity depends on soil texture and water management, but independent of crop type or N application rate. Both soil pH and organic C content were positively related to changes in bacterial diversity under N fertilization, while soil organic C was the dominant factor determining changes in bacterial diversity under NPK fertilization. Microbial biomass C decreased with decreasing bacterial diversity under long-term N fertilization. Nitrogen fertilization increased the relative abundance of copiotrophic bacteria (i.e. Proteobacteria and Actinobacteria), but reduced the abundance of oligotrophic taxa (i.e. Acidobacteria), consistent with the general life history strategy theory for bacteria. The relative abundance of Proteobacteria was also increased by NPK fertilization. The positive correlation between N application rate and the relative abundance of Actinobacteria indicates that increased N availability favored the growth of Actinobacteria. This first global analysis of long-term N and NPK fertilization effect on bacterial diversity and community composition suggests that N input decreases bacterial diversity but favors the growth of copiotrophic bacteria, providing a reference for nutrient management strategies for maintaining belowground microbial diversity

Long-term nitrogen fertilization decreases bacterial diversity and favors the growth of Actinobacteria and Proteobacteria in agro-ecosystems across the globe

DOE PAGES

Dai, Zhongmin; Su, Weiqin; Chen, Huaihai; ...

2018-04-25

Long-term Elevated nitrogen (N) input from anthropogenic sources may cause soil acidification and decrease crop yield, yet the response of the belowground microbial community to long-term N input and the input of N combined with phosphorus (P) and potassium (K) is still poorly understood. Here, we explored the effect of long-term N and NPK fertilization on soil bacterial diversity and community composition using meta-analysis of a global dataset. Nitrogen fertilization decreased soil pH, and increased soil organic carbon (C) and available N contents. Bacterial taxonomic diversity was decreased by N fertilization alone, but was increased by NPK fertilization. The effectmore » of N fertilization on bacterial diversity depends on soil texture and water management, but independent of crop type or N application rate. Both soil pH and organic C content were positively related to changes in bacterial diversity under N fertilization, while soil organic C was the dominant factor determining changes in bacterial diversity under NPK fertilization. Microbial biomass C decreased with decreasing bacterial diversity under long-term N fertilization. Nitrogen fertilization increased the relative abundance of copiotrophic bacteria (i.e. Proteobacteria and Actinobacteria), but reduced the abundance of oligotrophic taxa (i.e. Acidobacteria), consistent with the general life history strategy theory for bacteria. The relative abundance of Proteobacteria was also increased by NPK fertilization. The positive correlation between N application rate and the relative abundance of Actinobacteria indicates that increased N availability favored the growth of Actinobacteria. This first global analysis of long-term N and NPK fertilization effect on bacterial diversity and community composition suggests that N input decreases bacterial diversity but favors the growth of copiotrophic bacteria, providing a reference for nutrient management strategies for maintaining belowground microbial diversity

Volatile organic compound emissions from straw-amended agricultural soils and their relations to bacterial communities: A laboratory study.

PubMed

Zhao, Juan; Wang, Zhe; Wu, Ting; Wang, Xinming; Dai, Wanhong; Zhang, Yujie; Wang, Ran; Zhang, Yonggan; Shi, Chengfei

2016-07-01

A laboratory study was conducted to investigate volatile organic compound (VOC) emissions from agricultural soil amended with wheat straw and their associations with bacterial communities for a period of 66days under non-flooded and flooded conditions. The results indicated that ethene, propene, ethanol, i-propanol, 2-butanol, acetaldehyde, acetone, 2-butanone, 2-pentanone and acetophenone were the 10 most abundant VOCs, making up over 90% of the total VOCs released under the two water conditions. The mean emission of total VOCs from the amended soils under the non-flooded condition (5924ng C/(kg·hr)) was significantly higher than that under the flooded condition (2211ng C/(kg·hr)). One "peak emission window" appeared at days 0-44 or 4-44, and over 95% of the VOC emissions occurred during the first month under the two water conditions. Bacterial community analysis using denaturing gradient gel electrophoresis (DGGE) showed that a relative increase of Actinobacteria, Bacteroidetes, Firmicutes and γ-Proteobacteria but a relative decrease of Acidobacteria with time were observed after straw amendments under the two water conditions. Cluster analysis revealed that the soil bacterial communities changed greatly with incubation time, which was in line with the variation of the VOC emissions over the experimental period. Most of the above top 10 VOCs correlated positively with the predominant bacterial species of Bacteroidetes, Firmicutes and Verrucomicrobia but correlated negatively with the dominant bacterial species of Actinobacteria under the two water conditions. These results suggested that bacterial communities might play an important role in VOC emissions from straw-amended agricultural soils. Copyright © 2016. Published by Elsevier B.V.

Brazilian Cerrado soil Actinobacteria ecology.

PubMed

Suela Silva, Monique; Naves Sales, Alenir; Teixeira Magalhães-Guedes, Karina; Ribeiro Dias, Disney; Schwan, Rosane Freitas

2013-01-01

A total of 2152 Actinobacteria strains were isolated from native Cerrado (Brazilian Savannah) soils located in Passos, Luminárias, and Arcos municipalities (Minas Gerais State, Brazil). The soils were characterised for chemical and microbiological analysis. The microbial analysis led to the identification of nine genera (Streptomyces, Arthrobacter, Rhodococcus, Amycolatopsis, Microbacterium, Frankia, Leifsonia, Nakamurella, and Kitasatospora) and 92 distinct species in both seasons studied (rainy and dry). The rainy season produced a high microbial population of all the aforementioned genera. The pH values of the soil samples from the Passos, Luminárias, and Arcos regions varied from 4.1 to 5.5. There were no significant differences in the concentrations of phosphorus, magnesium, and organic matter in the soils among the studied areas. Samples from the Arcos area contained large amounts of aluminium in the rainy season and both hydrogen and aluminium in the rainy and dry seasons. The Actinobacteria population seemed to be unaffected by the high levels of aluminium in the soil. Studies are being conducted to produce bioactive compounds from Actinobacteria fermentations on different substrates. The present data suggest that the number and diversity of Actinobacteria spp. in tropical soils represent a vast unexplored resource for the biotechnology of bioactives production.

Brazilian Cerrado Soil Actinobacteria Ecology

PubMed Central

Suela Silva, Monique; Naves Sales, Alenir; Teixeira Magalhães-Guedes, Karina; Ribeiro Dias, Disney; Schwan, Rosane Freitas

2013-01-01

A total of 2152 Actinobacteria strains were isolated from native Cerrado (Brazilian Savannah) soils located in Passos, Luminárias, and Arcos municipalities (Minas Gerais State, Brazil). The soils were characterised for chemical and microbiological analysis. The microbial analysis led to the identification of nine genera (Streptomyces, Arthrobacter, Rhodococcus, Amycolatopsis, Microbacterium, Frankia, Leifsonia, Nakamurella, and Kitasatospora) and 92 distinct species in both seasons studied (rainy and dry). The rainy season produced a high microbial population of all the aforementioned genera. The pH values of the soil samples from the Passos, Luminárias, and Arcos regions varied from 4.1 to 5.5. There were no significant differences in the concentrations of phosphorus, magnesium, and organic matter in the soils among the studied areas. Samples from the Arcos area contained large amounts of aluminium in the rainy season and both hydrogen and aluminium in the rainy and dry seasons. The Actinobacteria population seemed to be unaffected by the high levels of aluminium in the soil. Studies are being conducted to produce bioactive compounds from Actinobacteria fermentations on different substrates. The present data suggest that the number and diversity of Actinobacteria spp. in tropical soils represent a vast unexplored resource for the biotechnology of bioactives production. PMID:23555089

Tungsten: A Preliminary Environmental Risk Assessment

DTIC Science & Technology

2011-05-01

Tungsten Effects on Soil Microbial Communities BUILDING STRONG® Actinobacteria Bacteroidetes Firmicutes alpha-Proteobacteria beta-Proteobacteria gamma...Persistence of Actinobacteria & gamma- Proteobacteria • Actinobacteria – includes the actinomycetes  γ-Proteobacteria – includes a variety of microbes

Comparison of the Rhizosphere Bacterial Communities of Zigongdongdou Soybean and a High-Methionine Transgenic Line of This Cultivar

PubMed Central

Ji, Jun; Wu, Haiying; Meng, Fang; Zhang, Mingrong; Zheng, Xiaobo; Wu, Cunxiang; Zhang, Zhengguang

2014-01-01

Previous studies have shown that methionine from root exudates affects the rhizosphere bacterial population involved in soil nitrogen fixation. A transgenic line of Zigongdongdou soybean cultivar (ZD91) that expresses Arabidopsis cystathionine γ-synthase resulting in an increased methionine production was examined for its influence to the rhizosphere bacterial population. Using 16S rRNA gene-based pyrosequencing analysis of the V4 region and DNA extracted from bacterial consortia collected from the rhizosphere of soybean plants grown in an agricultural field at the pod-setting stage, we characterized the populational structure of the bacterial community involved. In total, 87,267 sequences (approximately 10,908 per sample) were analyzed. We found that Acidobacteria, Proteobacteria, Bacteroidetes, Actinobacteria, Chloroflexi, Planctomycetes, Gemmatimonadetes, Firmicutes, and Verrucomicrobia constitute the dominant taxonomic groups in either the ZD91 transgenic line or parental cultivar ZD, and that there was no statistically significant difference in the rhizosphere bacterial community structure between the two cultivars. PMID:25079947

Culture-independent phylogenetic analysis of the microbial community in industrial sugarcane bagasse feedstock piles.

PubMed

Rattanachomsri, Ukrit; Kanokratana, Pattanop; Eurwilaichitr, Lily; Igarashi, Yasuo; Champreda, Verawat

2011-01-01

Sugarcane bagasse is an important lignocellulosic by-product with potential for conversion to biofuels and chemicals in biorefinery. As a step towards an understanding of microbial diversity and the processes existing in bagasse collection sites, the microbial community in industrial bagasse feedstock piles was investigated. Molecular biodiversity analysis of 16S rDNA sequences revealed the presence of a complex bacterial community. A diverse group of mainly aerobic and facultative anaerobic bacteria was identified reflecting the aerobic and high temperature microenvironmental conditions under the pile surface. The major bacterial taxa present were identified as Firmicutes, Alpha- and Gammaproteobacteria, Acidobacteria, Bacteroidetes, and Actinobacteria. Analysis of the eukaryotic microbial assemblage based on an internal transcribed spacer revealed the predominance of diverse cellulolytic and hemicellulolytic ascomycota. A microbial interaction model is proposed, focusing on lignocellulose degradation and methane metabolism. The insights into the microbial community in this study provide a basis for efficient utilization of bagasse in lignocellulosic biomass-based industries.

Epilithic and endolithic bacterial communities in limestone from a Maya archaeological site.

PubMed

McNamara, Christopher J; Perry, Thomas D; Bearce, Kristen A; Hernandez-Duque, Guillermo; Mitchell, Ralph

2006-01-01

Biodeterioration of archaeological sites and historic buildings is a major concern for conservators, archaeologists, and scientists involved in preservation of the world's cultural heritage. The Maya archaeological sites in southern Mexico, some of the most important cultural artifacts in the Western Hemisphere, are constructed of limestone. High temperature and humidity have resulted in substantial microbial growth on stone surfaces at many of the sites. Despite the porous nature of limestone and the common occurrence of endolithic microorganisms in many habitats, little is known about the microbial flora living inside the stone. We found a large endolithic bacterial community in limestone from the interior of the Maya archaeological site Ek' Balam. Analysis of 16S rDNA clones demonstrated disparate communities (endolithic: >80% Actinobacteria, Acidobacteria, and Low GC Firmicutes; epilithic: >50% Proteobacteria). The presence of differing epilithic and endolithic bacterial communities may be a significant factor for conservation of stone cultural heritage materials and quantitative prediction of carbonate weathering.

Population densities of indigenous Acidobacteria change in the presence of plant growth promoting rhizobacteria (PGPR) in rhizosphere.

PubMed

Kalam, Sadaf; Das, Subha Narayan; Basu, Anirban; Podile, Appa Rao

2017-05-01

Rhizosphere microbial community has diverse metabolic capabilities and plays a crucial role in maintaining plant health. Oligotrophic plant growth promoting rhizobacteria (PGPR), along with difficult-to-culture microbial fractions, might be involved synergistically in microbe-microbe and plant-microbe interactions in the rhizosphere. Among the difficult-to-culture microbial fractions, Acidobacteria constitutes the most dominant phylum thriving in rhizospheric soils. We selected effective PGPR for tomato and black gram and studied their effect on population densities of acidobacterial members. Three facultatively oligotrophic PGPR were identified through 16S rRNA gene sequencing as Sphingobacterium sp. (P3), Variovorax sp. (P4), and Roseomonas sp. (A2); the latter being a new report of PGPR. In presence of selected PGPR strains, the changes in population densities of Acidobacteria were monitored in metagenomic DNA extracted from bulk and rhizospheric soils of tomato and black gram using real time qPCR. A gradual increase in equivalent cell numbers of Acidobacteria members was observed over time along with a simultaneous increase in plant growth promotion by test PGPR. We report characterization of three effective PGPR strains and their effects on indigenous, underexplored difficult-to-culture phylum-Acidobacteria. We suggest that putative interactions between these two bacterial groups thriving in rhizospheric soils could be beneficial for plant growth. © 2017 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

Penicillin-binding proteins in Actinobacteria.

PubMed

Ogawara, Hiroshi

2015-04-01

Because some Actinobacteria, especially Streptomyces species, are β-lactam-producing bacteria, they have to have some self-resistant mechanism. The β-lactam biosynthetic gene clusters include genes for β-lactamases and penicillin-binding proteins (PBPs), suggesting that these are involved in self-resistance. However, direct evidence for the involvement of β-lactamases does not exist at the present time. Instead, phylogenetic analysis revealed that PBPs in Streptomyces are distinct in that Streptomyces species have much more PBPs than other Actinobacteria, and that two to three pairs of similar PBPs are present in most Streptomyces species examined. Some of these PBPs bind benzylpenicillin with very low affinity and are highly similar in their amino-acid sequences. Furthermore, other low-affinity PBPs such as SCLAV_4179 in Streptomyces clavuligerus, a β-lactam-producing Actinobacterium, may strengthen further the self-resistance against β-lactams. This review discusses the role of PBPs in resistance to benzylpenicillin in Streptomyces belonging to Actinobacteria.

Taxonomy, Physiology, and Natural Products of Actinobacteria

PubMed Central

Vatsa, Parul; Sanchez, Lisa; Gaveau-Vaillant, Nathalie; Jacquard, Cedric; Klenk, Hans-Peter; Clément, Christophe; Ouhdouch, Yder

2015-01-01

SUMMARY Actinobacteria are Gram-positive bacteria with high G+C DNA content that constitute one of the largest bacterial phyla, and they are ubiquitously distributed in both aquatic and terrestrial ecosystems. Many Actinobacteria have a mycelial lifestyle and undergo complex morphological differentiation. They also have an extensive secondary metabolism and produce about two-thirds of all naturally derived antibiotics in current clinical use, as well as many anticancer, anthelmintic, and antifungal compounds. Consequently, these bacteria are of major importance for biotechnology, medicine, and agriculture. Actinobacteria play diverse roles in their associations with various higher organisms, since their members have adopted different lifestyles, and the phylum includes pathogens (notably, species of Corynebacterium, Mycobacterium, Nocardia, Propionibacterium, and Tropheryma), soil inhabitants (e.g., Micromonospora and Streptomyces species), plant commensals (e.g., Frankia spp.), and gastrointestinal commensals (Bifidobacterium spp.). Actinobacteria also play an important role as symbionts and as pathogens in plant-associated microbial communities. This review presents an update on the biology of this important bacterial phylum. PMID:26609051

Thermophilic and alkaliphilic Actinobacteria: biology and potential applications

PubMed Central

Shivlata, L.; Satyanarayana, Tulasi

2015-01-01

Microbes belonging to the phylum Actinobacteria are prolific sources of antibiotics, clinically useful bioactive compounds and industrially important enzymes. The focus of the current review is on the diversity and potential applications of thermophilic and alkaliphilic actinobacteria, which are highly diverse in their taxonomy and morphology with a variety of adaptations for surviving and thriving in hostile environments. The specific metabolic pathways in these actinobacteria are activated for elaborating pharmaceutically, agriculturally, and biotechnologically relevant biomolecules/bioactive compounds, which find multifarious applications. PMID:26441937

Isolation of antimicrobial producing Actinobacteria from soil samples.

PubMed

Elbendary, Afaf Ahmed; Hessain, Ashgan Mohamed; El-Hariri, Mahmoud Darderi; Seida, Ahmed Adel; Moussa, Ihab Mohamed; Mubarak, Ayman Salem; Kabli, Saleh A; Hemeg, Hassan A; El Jakee, Jakeen Kamal

2018-01-01

Emergence of multidrug resistant bacteria has made the search for novel bioactive compounds from natural and unexplored habitats a necessity. Actinobacteria have important bioactive substances. The present study investigated antimicrobial activity of Actinobacteria isolated from soil samples of Egypt. One hundred samples were collected from agricultural farming soil of different governorates. Twelve isolates have produced activity against the tested microorganisms ( S. aureus , Bacillus cereus , E. coli , K. pneumoniae , P. aeruginosa , S. Typhi, C. albicans , A. niger and A. flavus ). By VITEK 2 system version: 07.01 the 12 isolates were identified as Kocuria kristinae , Kocuria rosea , Streptomyces griseus , Streptomyces flaveolus and Actinobacteria . Using ethyl acetate extraction method the isolates culture's supernatants were tested by diffusion method against indicator microorganisms. These results indicate that Actinobacteria isolated from Egypt farms could be sources of antimicrobial bioactive substances.

Chitinolytic functions in actinobacteria: ecology, enzymes, and evolution.

PubMed

Lacombe-Harvey, Marie-Ève; Brzezinski, Ryszard; Beaulieu, Carole

2018-06-21

Actinobacteria, a large group of Gram-positive bacteria, secrete a wide range of extracellular enzymes involved in the degradation of organic compounds and biopolymers including the ubiquitous aminopolysaccharides chitin and chitosan. While chitinolytic enzymes are distributed in all kingdoms of life, actinobacteria are recognized as particularly good decomposers of chitinous material and several members of this taxon carry impressive sets of genes dedicated to chitin and chitosan degradation. Degradation of these polymers in actinobacteria is dependent on endo- and exo-acting hydrolases as well as lytic polysaccharide monooxygenases. Actinobacterial chitinases and chitosanases belong to nine major families of glycosyl hydrolases that share no sequence similarity. In this paper, the distribution of chitinolytic actinobacteria within different ecosystems is examined and their chitinolytic machinery is described and compared to those of other chitinolytic organisms.

Diversity and distribution of Actinobacteria associated with reef coral Porites lutea

PubMed Central

Kuang, Weiqi; Li, Jie; Zhang, Si; Long, Lijuan

2015-01-01

Actinobacteria is a ubiquitous major group in coral holobiont. The diversity and spatial and temporal distribution of actinobacteria have been rarely documented. In this study, diversity of actinobacteria associated with mucus, tissue and skeleton of Porites lutea and in the surrounding seawater were examined every 3 months for 1 year on Luhuitou fringing reef. The population structures of the P. lutea-associated actinobacteria were analyzed using phylogenetic analysis of 16S rRNA gene clone libraries, which demonstrated highly diverse actinobacteria profiles in P. lutea. A total of 25 described families and 10 unnamed families were determined in the populations, and 12 genera were firstly detected in corals. The Actinobacteria diversity was significantly different between the P. lutea and the surrounding seawater. Only 10 OTUs were shared by the seawater and coral samples. Redundancy and hierarchical cluster analyses were performed to analyze the correlation between the variations of actinobacteria population within the divergent compartments of P. lutea, seasonal changes, and environmental factors. The actinobacteria communities in the same coral compartment tended to cluster together. Even so, an extremely small fraction of OTUs was common in all three P. lutea compartments. Analysis of the relationship between actinobacteria assemblages and the environmental parameters showed that several genera were closely related to specific environmental factors. This study highlights that coral-associated actinobacteria populations are highly diverse, and spatially structured within P. lutea, and they are distinct from which in the ambient seawater. PMID:26539166

[Diversity of cultivable actinobacteria in Xinghu wetland sediments].

PubMed

Xue, Dong; Zhao, Guozhen; Yao, Qing; Zhao, Haiquan; Zhu, Honghui

2015-11-04

To study the diversity of cultivable actinobacteria in Xinghu wetland and screen actinobacteria with a pharmaceutical potential for producing biologically active secondary metabolites. We studied the diversity of actinobacteria isolated from Xinghu wetland by using different selective isolation media and methods. The high bioactive actinobacteria were identified and further investigated for the presence of polyketide synthases (PKS-I, PKS-II), nonribosomal peptide synthetases (NRPS), 3-amino-5-hydroxybenzoic acid synthases (AHBA) and 3-hydroxy-3-methylglutaryl Coenzyme A (HMG CoA) sequences by specific amplification. More than 300 actinobacteria were isolated, and 135 isolates were selected on the basis of their morphologies on different media and were further characterized by 16S rRNA gene sequencing. The isolates belonged to 7 orders, 10 families, 13 genera, Streptomyces was the most frequently isolated genus, followed by the genera Micromonospora and Nocardia. Twenty-four isolates showed high activity against Staphylococcus aureus and Escherichia coli, but there no strain displaying antagonistic activity against Salmonella sp. High frequencies of positive PCR amplification were obtained for PKS-I (16.7%, 4/24), PKS-II (62.5%,15/24), NRPS (16.7%, 4/24), HMG CoA (29.2%, 7/24) and AHBA (12.5%, 3/24) biosynthetic systems. High Performance Liquid Chromatography showed that strain XD7, XD114, XD128 produce lots of secondary metabolites. This study indicated that actinobacteria isolated from Xinghu wetland are abundant and have potentially beneficial and diverse bioactivities which should be pursued for their biotechnical promise.

Coral-Associated Actinobacteria: Diversity, Abundance, and Biotechnological Potentials

PubMed Central

Mahmoud, Huda M.; Kalendar, Aisha A.

2016-01-01

Marine Actinobacteria, particularly coral-associated Actinobacteria, have attracted attention recently. In this study, the abundance and diversity of Actinobacteria associated with three types of coral thriving in a thermally stressed coral reef system north of the Arabian Gulf were investigated. Coscinaraea columna, Platygyra daedalea and Porites harrisoni have been found to harbor equivalent numbers of culturable Actinobacteria in their tissues but not in their mucus. However, different culturable actinobacterial communities have been found to be associated with different coral hosts. Differences in the abundance and diversity of Actinobacteria were detected between the mucus and tissue of the same coral host. In addition, temporal and spatial variations in the abundance and diversity of the cultivable actinobacterial communities were detected. In total, 19 different actinobacterial genera, namely Micrococcus, Brachybacterium, Brevibacterium, Streptomyces, Micromonospora, Renibacterium, Nocardia, Microbacterium, Dietzia, Cellulomonas, Ornithinimicrobium, Rhodococcus, Agrococcus, Kineococcus, Dermacoccus, Devriesea, Kocuria, Marmoricola, and Arthrobacter, were isolated from the coral tissue and mucus samples. Furthermore, 82 isolates related to Micromonospora, Brachybacterium, Nocardia, Micrococcus, Arthrobacter, Rhodococcus, and Streptomyces showed antimicrobial activities against representative Gram-positive and/or Gram-negative bacteria. Even though Brevibacterium and Kocuria were the most dominant actinobacterial isolates, they failed to show any antimicrobial activity, whereas less dominant genera, such as Streptomyces, did show antimicrobial activity. Focusing on the diversity of coral-associated Actinobacteria may help to understand how corals thrive under harsh environmental conditions and may lead to the discovery of novel antimicrobial metabolites with potential biotechnological applications. PMID:26973601

Taxonomy, Physiology, and Natural Products of Actinobacteria.

PubMed

Barka, Essaid Ait; Vatsa, Parul; Sanchez, Lisa; Gaveau-Vaillant, Nathalie; Jacquard, Cedric; Meier-Kolthoff, Jan P; Klenk, Hans-Peter; Clément, Christophe; Ouhdouch, Yder; van Wezel, Gilles P

2016-03-01

Actinobacteria are Gram-positive bacteria with high G+C DNA content that constitute one of the largest bacterial phyla, and they are ubiquitously distributed in both aquatic and terrestrial ecosystems. Many Actinobacteria have a mycelial lifestyle and undergo complex morphological differentiation. They also have an extensive secondary metabolism and produce about two-thirds of all naturally derived antibiotics in current clinical use, as well as many anticancer, anthelmintic, and antifungal compounds. Consequently, these bacteria are of major importance for biotechnology, medicine, and agriculture. Actinobacteria play diverse roles in their associations with various higher organisms, since their members have adopted different lifestyles, and the phylum includes pathogens (notably, species of Corynebacterium, Mycobacterium, Nocardia, Propionibacterium, and Tropheryma), soil inhabitants (e.g., Micromonospora and Streptomyces species), plant commensals (e.g., Frankia spp.), and gastrointestinal commensals (Bifidobacterium spp.). Actinobacteria also play an important role as symbionts and as pathogens in plant-associated microbial communities. This review presents an update on the biology of this important bacterial phylum. Copyright © 2015, American Society for Microbiology. All Rights Reserved.

Marine actinobacteria as a drug treasure house.

PubMed

Hassan, Syed Shams Ul; Shaikh, Abdul Lateef

2017-03-01

Marine actinobacteria have been considered as a gold mine with respect to great potential regarding their secondary metabolites. Most of the researches have been conducted on actinobacteria's derived secondary metabolites to examine its pharmacological properties. Actinobacteria have a potential to provide future drugs against crucial diseases, such as drug-resistance bacteria, cancer, a range of viral illnesses, malaria, several infections and inflammations. Although, the mode of action of many bio molecules are still untapped, for a tangible number of compounds by which they interfere with human pathogenesis are reported here with detailed diagrammed illustrations. This knowledge is one of the basic vehicles to be known especially for transforming bio medicinal molecules to medicines. Actinobacteria produce a different kind of biochemical substances with numerous carbon skeletons, which have been found to be the main component interfering with human pathogenesis at different sites. Different diseases have the capability to fight at different sites inside the body can lead to a new wave of increasing the chances to produce targeted medicines. Copyright © 2016 Elsevier Masson SAS. All rights reserved.

Phylogenetic diversity of culturable bacteria in surface seawater from the Drake Passage, Antarctica

NASA Astrophysics Data System (ADS)

Li, Zhao; Xing, Mengxin; Wang, Wei; Wang, Dan; Zhu, Jiancheng; Sun, Mi

2016-09-01

The Drake Passage is located between the Antarctic Peninsula and Tierra del Fuego in the south of South America. Surface seawater samples were collected at seven sites in the Drake Passage during the austral summer of 2012. The 16S rRNA sequences were analyzed from 187 isolated bacterial strains. Three phyla, 29 genera and 56 species were identified. The three phyla were Actinobacteria, Firmicutes and Proteobacteria; the Proteobacteria included α-Proteobacteria, β-Proteobacteria and γ-Proteobacteria. γ-Proteobacteria, Actinobacteria and Firmicutes were the dominant class or phyla in terms of quantity and species. Gram-positive bacteria (Actinobacteria and Firmicutes) accounted for 57.8% of all types identified. There were nine dominant genera, including Curtobacterium, Staphylococcus, and Halomonas, and 14 dominant species including Curtobacterium flaccumfaciens, Curtobacterium pusillum, and Staphylococcus sciuri. Of the strains identified, 87.2% were catalase positive or weakly positive.

Research on marine actinobacteria in India.

PubMed

Sivakumar, K; Sahu, Maloy Kumar; Thangaradjou, T; Kannan, L

2007-09-01

Marine actinobacteriology is one of the major emerging areas of research in tropics. Marine actinobacteria occur on the sediments and in water and also other biomass (mangrove) and substrates (animal). These organisms are gaining importance not only for their taxonomic and ecological perspectives, but also for their unique metabolites and enzymes. Many earlier studies on these organisms were confined only to the temperate regions. In tropical environment, investigations on them have gained importance only in the last two decades. So far, from the Indian peninsula, 41 species of actinobacteria belonging to 8 genera have been recorded. The genus, Streptomyces of marine origin has been more frequently recorded. Of 9 maritime states of India, only 4 have been extensively covered for the study of marine actinobacteria. Most of the studies conducted pertain to isolation, identification and maintenance of these organisms in different culture media. Further, attention has been focused on studying their antagonistic properties against different pathogens. Their biotechnological potentials are yet to be fully explored.

Firmicutes dominate the bacterial taxa within sugar-cane processing plants

PubMed Central

Sharmin, Farhana; Wakelin, Steve; Huygens, Flavia; Hargreaves, Megan

2013-01-01

Sugar cane processing sites are characterised by high sugar/hemicellulose levels, available moisture and warm conditions, and are relatively unexplored unique microbial environments. The PhyloChip microarray was used to investigate bacterial diversity and community composition in three Australian sugar cane processing plants. These ecosystems were highly complex and dominated by four main Phyla, Firmicutes (the most dominant), followed by Proteobacteria, Bacteroidetes, and Chloroflexi. Significant variation (p < 0.05) in community structure occurred between samples collected from ‘floor dump sediment’, ‘cooling tower water’, and ‘bagasse leachate’. Many bacterial Classes contributed to these differences, however most were of low numerical abundance. Separation in community composition was also linked to Classes of Firmicutes, particularly Bacillales, Lactobacillales and Clostridiales, whose dominance is likely to be linked to their physiology as ‘lactic acid bacteria’, capable of fermenting the sugars present. This process may help displace other bacterial taxa, providing a competitive advantage for Firmicutes bacteria. PMID:24177592

Actinobacteria from Arid and Desert Habitats: Diversity and Biological Activity

PubMed Central

Mohammadipanah, Fatemeh; Wink, Joachim

2016-01-01

The lack of new antibiotics in the pharmaceutical pipeline guides more and more researchers to leave the classical isolation procedures and to look in special niches and ecosystems. Bioprospecting of extremophilic Actinobacteria through mining untapped strains and avoiding resiolation of known biomolecules is among the most promising strategies for this purpose. With this approach, members of acidtolerant, alkalitolerant, psychrotolerant, thermotolerant, halotolerant and xerotolerant Actinobacteria have been obtained from respective habitats. Among these, little survey exists on the diversity of Actinobacteria in arid areas, which are often adapted to relatively high temperatures, salt concentrations, and radiation. Therefore, arid and desert habitats are special ecosystems which can be recruited for the isolation of uncommon Actinobacteria with new metabolic capability. At the time of this writing, members of Streptomyces, Micromonospora, Saccharothrix, Streptosporangium, Cellulomonas, Amycolatopsis, Geodermatophilus, Lechevalieria, Nocardia, and Actinomadura are reported from arid habitats. However, metagenomic data present dominant members of the communities in desiccating condition of areas with limited water availability that are not yet isolated. Furthermore, significant diverse types of polyketide synthase (PKS) and non-ribosomal peptide synthetase (NRPS) genes are detected in xerophilic and xerotolerant Actinobacteria and some bioactive compounds are reported from them. Rather than pharmaceutically active metabolites, molecules with protection activity against drying such as Ectoin and Hydroxyectoin with potential application in industry and agriculture have also been identified from xerophilic Actinobacteria. In addition, numerous biologically active small molecules are expected to be discovered from arid adapted Actinobacteria in the future. In the current survey, the diversity and biotechnological potential of Actinobacteria obtained from arid ecosystems

Rational synthetic pathway refactoring of natural products biosynthesis in actinobacteria.

PubMed

Tan, Gao-Yi; Liu, Tiangang

2017-01-01

Natural products (NPs) and their derivatives are widely used as frontline treatments for many diseases. Actinobacteria spp. are used to produce most of NP antibiotics and have also been intensively investigated for NP production, derivatization, and discovery. However, due to the complicated transcriptional and metabolic regulation of NP biosynthesis in Actinobacteria, especially in the cases of genome mining and heterologous expression, it is often difficult to rationally and systematically engineer synthetic pathways to maximize biosynthetic efficiency. With the emergence of new tools and methods in metabolic engineering, the synthetic pathways of many chemicals, such as fatty acids and biofuels, in model organisms (e.g. Escherichia coli ), have been refactored to realize precise and flexible control of production. These studies also offer a promising approach for synthetic pathway refactoring in Actinobacteria. In this review, the great potential of Actinobacteria as a microbial cell factory for biosynthesis of NPs is discussed. To this end, recent progress in metabolic engineering of NP synthetic pathways in Actinobacteria are summarized and strategies and perspectives to rationally and systematically refactor synthetic pathways in Actinobacteria are highlighted. Copyright © 2016 The Authors. Published by Elsevier Inc. All rights reserved.

Microdiversification in genome-streamlined ubiquitous freshwater Actinobacteria.

PubMed

Neuenschwander, Stefan M; Ghai, Rohit; Pernthaler, Jakob; Salcher, Michaela M

2018-01-01

Actinobacteria of the acI lineage are the most abundant microbes in freshwater systems, but there are so far no pure living cultures of these organisms, possibly because of metabolic dependencies on other microbes. This, in turn, has hampered an in-depth assessment of the genomic basis for their success in the environment. Here we present genomes from 16 axenic cultures of acI Actinobacteria. The isolates were not only of minute cell size, but also among the most streamlined free-living microbes, with extremely small genome sizes (1.2-1.4 Mbp) and low genomic GC content. Genome reduction in these bacteria might have led to auxotrophy for various vitamins, amino acids and reduced sulphur sources, thus creating dependencies to co-occurring organisms (the 'Black Queen' hypothesis). Genome analyses, moreover, revealed a surprising degree of inter- and intraspecific diversity in metabolic pathways, especially of carbohydrate transport and metabolism, and mainly encoded in genomic islands. The striking genotype microdiversification of acI Actinobacteria might explain their global success in highly dynamic freshwater environments with complex seasonal patterns of allochthonous and autochthonous carbon sources. We propose a new order within Actinobacteria ('Candidatus Nanopelagicales') with two new genera ('Candidatus Nanopelagicus' and 'Candidatus Planktophila') and nine new species.

A new approach to isolating siderophore-producing actinobacteria.

PubMed

Nakouti, I; Sihanonth, P; Hobbs, G

2012-07-01

This study was conducted to investigate the application of 2,2'-dipyridyl as a new approach to isolating siderophore-producing actinobacteria. Isolation of actinobacteria from soil was conducted by a soil dilution plate technique using starch-casein agar. Iron starvation was fostered by the incorporation of the iron chelator 2,2'-dipyridyl in the isolation medium. Pretreatment of the samples at an elevated temperature (40°C) ensured that the majority of nonsporulating bacteria were excluded. The survivors of this treatment were largely actinobacteria. Of the viable cultures grown in the presence of 2,2'-dipyridyl, more than 78-88% (average of three separate studies) were reported to produce siderophore-like compounds compared to 13-18% (average of three separate studies) when grown on the basic media in the absence of the chelating agent. The most prolific producers as assessed by the chrome azurol sulphate (CAS) assay were further characterized and found to belong to the genus Streptomyces. Selective pressure using 2,2'-dipyridyl as an iron-chelating agent in starch-casein media increased the isolation of siderophore-producing actinobacteria compared to the unamended medium. The study described represents a new approach to the isolation of siderophore-producing actinobacteria using a novel procedure that places a selection on cell population based upon the incorporation of a chelating agent in the medium. © 2012 The Authors. Letters in Applied Microbiology © 2012 The Society for Applied Microbiology.

Antimicrobial Activity of Actinobacteria Isolated From the Guts of Subterranean Termites

PubMed Central

Arango, R. A.; Carlson, C. M.; Currie, C. R.; McDonald, B. R.; Book, A. J.; Green, F.; Lebow, N. K.; Raffa, K. F.

2016-01-01

Subterranean termites need to minimize potentially pathogenic and competitive fungi in their environment in order to maintain colony health. We examined the ability of Actinobacteria isolated from termite guts in suppressing microorganisms commonly encountered in a subterranean environment. Guts from two subterranean termite species, Reticulitermes flavipes (Kollar) and Reticulitermes tibialis Banks, were extracted and plated on selective chitin media. A total of 38 Actinobacteria isolates were selected for in vitro growth inhibition assays. Target microbes included three strains of Serratia marcescens Bizio, two mold fungi (Trichoderma sp. and Metarhizium sp.), a yeast fungus (Candida albicans (C.P. Robin) Berkhout), and four basidiomycete fungi (Gloeophyllum trabeum (Persoon) Murrill, Tyromyces palustris (Berkeley & M.A. Curtis) Murrill, Irpex lacteus (Fries) Fries, and Trametes versicolor (L.) Lloyd). Results showed both broad and narrow ranges of antimicrobial activity against the mold fungi, yeast fungus, and S. marcescens isolates by the Actinobacteria selected. This suggests that termite gut-associated Actinobacteria produce secondary antimicrobial compounds that may be important for pathogen inhibition in termites. Basidiomycete fungi were strongly inhibited by the selected Actinobacteria isolates, with G. trabeum and T. versicolor being most inhibited, followed by I. lacteus and T. palustris. The degree of inhibition was correlated with shifts in pH caused by the Actinobacteria. Nearly all Actinobacteria isolates raised pH of the growth medium to basic levels (i.e. pH ∼8.0–9.5). We summarize antimicrobial activity of these termite gut-associated Actinobacteria and examine the implications of these pH shifts. PMID:28028088

Biomedical Applications of Enzymes From Marine Actinobacteria.

PubMed

Kamala, K; Sivaperumal, P

Marine microbial enzyme technologies have progressed significantly in the last few decades for different applications. Among the various microorganisms, marine actinobacterial enzymes have significant active properties, which could allow them to be biocatalysts with tremendous bioactive metabolites. Moreover, marine actinobacteria have been considered as biofactories, since their enzymes fulfill biomedical and industrial needs. In this chapter, the marine actinobacteria and their enzymes' uses in biological activities and biomedical applications are described. © 2017 Elsevier Inc. All rights reserved.

Microbial diversity at the moderate acidic stage in three different sulfidic mine tailings dumps generating acid mine drainage.

PubMed

Korehi, Hananeh; Blöthe, Marco; Schippers, Axel

2014-11-01

In freshly deposited sulfidic mine tailings the pH is alkaline or circumneutral. Due to pyrite or pyrrhotite oxidation the pH is dropping over time to pH values <3 at which acidophilic iron- and sulfur-oxidizing prokaryotes prevail and accelerate the oxidation processes, well described for several mine waste sites. The microbial communities at the moderate acidic stage in mine tailings are only scarcely studied. Here we investigated the microbial diversity via 16S rRNA gene sequence analysis in eight samples (pH range 3.2-6.5) from three different sulfidic mine tailings dumps in Botswana, Germany and Sweden. In total 701 partial 16S rRNA gene sequences revealed a divergent microbial community between the three sites and at different tailings depths. Proteobacteria and Firmicutes were overall the most abundant phyla in the clone libraries. Acidobacteria, Actinobacteria, Bacteroidetes, and Nitrospira occurred less frequently. The found microbial communities were completely different to microbial communities in tailings at

Bacterial Diversity in Bentonites, Engineered Barrier for Deep Geological Disposal of Radioactive Wastes.

PubMed

Lopez-Fernandez, Margarita; Cherkouk, Andrea; Vilchez-Vargas, Ramiro; Jauregui, Ruy; Pieper, Dietmar; Boon, Nico; Sanchez-Castro, Ivan; Merroun, Mohamed L

2015-11-01

The long-term disposal of radioactive wastes in a deep geological repository is the accepted international solution for the treatment and management of these special residues. The microbial community of the selected host rocks and engineered barriers for the deep geological repository may affect the performance and the safety of the radioactive waste disposal. In this work, the bacterial population of bentonite formations of Almeria (Spain), selected as a reference material for bentonite-engineered barriers in the disposal of radioactive wastes, was studied. 16S ribosomal RNA (rRNA) gene-based approaches were used to study the bacterial community of the bentonite samples by traditional clone libraries and Illumina sequencing. Using both techniques, the bacterial diversity analysis revealed similar results, with phylotypes belonging to 14 different bacterial phyla: Acidobacteria, Actinobacteria, Armatimonadetes, Bacteroidetes, Chloroflexi, Cyanobacteria, Deinococcus-Thermus, Firmicutes, Gemmatimonadetes, Planctomycetes, Proteobacteria, Nitrospirae, Verrucomicrobia and an unknown phylum. The dominant groups of the community were represented by Proteobacteria and Bacteroidetes. A high diversity was found in three of the studied samples. However, two samples were less diverse and dominated by Betaproteobacteria.

Rapid aerobic granulation in an SBR treating piggery wastewater by seeding sludge from a municipal WWTP.

PubMed

Liu, Jun; Li, Jun; Wang, Xiaodong; Zhang, Qi; Littleton, Helen

2017-01-01

Aerobic sludge granulation was rapidly obtained in the erlenmeyer bottle and sequencing batch reactor (SBR) using piggery wastewater. Aerobic granulation occurred on day 3 and granules with mean diameter of 0.2mm and SVI 30 of 20.3mL/g formed in SBR on day 18. High concentrations of Ca and Fe in the raw piggery wastewater and operating mode accelerated aerobic granulation, even though the seed sludge was from a municipal wastewater treatment plant (WWTP). Alpha diversity analysis revealed Operational Taxonomic Units, Shannon, ACE and Chao 1 indexes in aerobic granules were 2013, 5.51, 4665.5 and 3734.5, which were obviously lower compared to seed sludge. The percentages of major microbial communities, such as Proteobacteria, Bacteroidetes and Firmicutes were obviously higher in aerobic granules than seed sludge. Chloroflexi, Planctomycetes, Actinobacteria, TM7 and Acidobacteria showed much higher abundances in the inoculum. The main reasons might be the characteristics of raw piggery wastewater and granule structure. Copyright © 2016. Published by Elsevier B.V.

Dynamics and diversity of the bacterial community during the spontaneous decay of açai (Euterpe oleracea) fruits.

PubMed

Moura, Fábio Gomes; Graças, Diego Assis das; Santos, Agenor Valadares; Silva, Artur Luiz da Costa da; Rogez, Hervé

2018-04-30

The biodiversity and evolution of the microbial community in açai fruits (AF) between three geographical origins and two spontaneous decay conditions were examined by applying culture-independent methods. Culture-independent methods based on 16S rRNA from fifteen samples revealed that Proteobacteria, Firmicutes, Actinobacteria, Bacteroidetes and Acidobacteria were the most abundant phyla. At the genus level, Massilia (taxon with more than 50% of the sequences remaining constant during the 30h of decay), Pantoea, Naxibacter, Enterobacter, Raoultella and Klebsiella were identified, forming the carposphere bacterial microbiota of AF. AF is fibre-rich and Massilia bacteria could find a large quantity of substrate for its growth through cellulase production. Beta diversity showed that the quality parameters of AF (pH, soluble solids, titratable acidity and lipids) and elemental analysis (C, N, H and C/N ratio) were unable to drive microbial patterns in AF. This research offers new insight into the indigenous bacterial community composition on AF as a function of spontaneous postharvest decay. Copyright © 2018 Sociedade Brasileira de Microbiologia. Published by Elsevier Editora Ltda. All rights reserved.

Microbial mat of the thermal springs Kuchiger Republic of Buryatia: species composition, biochemical properties and electrogenic activity in biofuel cell

NASA Astrophysics Data System (ADS)

Aleksandrovich Yuriev, Denis; Viktorovna Zaitseva, Svetlana; Olegovna Zhdanova, Galina; Yurievich Tolstoy, Mikhail; Dondokovna Barkhutova, Darima; Feodorovna Vyatchina, Olga; Yuryevna Konovalova, Elena; Iosifovich Stom, Devard

2018-02-01

Electrogenic, molecular and some other properties of a microbial mat isolated from the Kuchiger hot spring (Kurumkansky District, Republic of Buryatia) were studied. Molecular analysis showed that representatives of Proteobacteria (85.5 % of the number of classified bacterial sequences) prevailed in the microbial mat of the Kuchiger springs, among which sulfur bacteria of the genus Thiothrix were the most numerous. In the microbial mat there were bacteria from the families Rhodocyclaceae, Comamonadaceae and Flavobacteriaceae. Phylum Bacteroidetes, Cyanobacteria/Chloroplast, Fusobacteria, Fibrobacteres, Acidobacteria, Chlorobi, Spirochaetes, Verrucomicrobia, Firmicutes, Deinococcus-Thermus, Chloroflexi and Actinobacteria are also noted in the composition of the microbial mat. Under the experimental conditions using Kuchiger-mat 16 as bioagents, glucose and peptone as substrates, the power of BFC was 240 and 221 mW / m2, respectively. When replacing the substrate with sodium acetate, the efficiency of the BFC was reduced by a factor of 10 (20 mW / m2). The prospects of using a microbial mat “Kuchiger-16” as an electrogen in BFC when utilizing alkaline waste water components to generate electricity are discussed.

Marine actinobacteria: an important source of bioactive natural products.

PubMed

Manivasagan, Panchanathan; Kang, Kyong-Hwa; Sivakumar, Kannan; Li-Chan, Eunice C Y; Oh, Hyun-Myung; Kim, Se-Kwon

2014-07-01

Marine environment is largely an untapped source for deriving actinobacteria, having potential to produce novel, bioactive natural products. Actinobacteria are the prolific producers of pharmaceutically active secondary metabolites, accounting for about 70% of the naturally derived compounds that are currently in clinical use. Among the various actinobacterial genera, Actinomadura, Actinoplanes, Amycolatopsis, Marinispora, Micromonospora, Nocardiopsis, Saccharopolyspora, Salinispora, Streptomyces and Verrucosispora are the major potential producers of commercially important bioactive natural products. In this respect, Streptomyces ranks first with a large number of bioactive natural products. Marine actinobacteria are unique enhancing quite different biological properties including antimicrobial, anticancer, antiviral, insecticidal and enzyme inhibitory activities. They have attracted global in the last ten years for their ability to produce pharmaceutically active compounds. In this review, we have focused attention on the bioactive natural products isolated from marine actinobacteria, possessing unique chemical structures that may form the basis for synthesis of novel drugs that could be used to combat resistant pathogenic microorganisms. Copyright © 2014 Elsevier B.V. All rights reserved.

[Diversity and bioactivity of culturable actinobacteria from animal feces].

PubMed

Jiang, Yi; Cao, Yanru; Han, Li; Jin, Rongxian; Zheng, Dan; He, Wenxiang; Li, Youlong; Huang, Xueshi

2012-10-04

In order to provide new source for discovering new lead compounds of drugs and other products, the diversity and some bioactivities of culturable actinobacteria in animal feces were studied. Five animals' fecal samples were collected from Yunnan Wild Animal Park. The pure cultures of actinobacteria were isolated from these samples by using 5 different media. The 16S rRNA gene sequences of 119 selected strains were determined; the phylogenetic analysis was carried out; and antimicrobial and anti-tumor activities were determined by using agar diffusion method, tumor cell lines k562and HL60 respectively. In total 20 genera of actinobacteria from the 5 animals' feces were identified. Many strains inhibited Bacillus subtilis, Staphylococcus lentus, Mycobacterium tuberculosis, Candida albicans and Aspergillus niger. Some strains presented antitumor activities. Some known secondary metabolites and Sannastatin, a novel macrolactam polyketide glycoside with bioactivities, were isolated and identified. Fecal actinobacteria are a new potential source for discovering drug lead and other industry products.

Metagenomic recovery of phage genomes of uncultured freshwater actinobacteria.

PubMed

Ghai, Rohit; Mehrshad, Maliheh; Mizuno, Carolina Megumi; Rodriguez-Valera, Francisco

2017-01-01

Low-GC Actinobacteria are among the most abundant and widespread microbes in freshwaters and have largely resisted all cultivation efforts. Consequently, their phages have remained totally unknown. In this work, we have used deep metagenomic sequencing to assemble eight complete genomes of the first tailed phages that infect freshwater Actinobacteria. Their genomes encode the actinobacterial-specific transcription factor whiB, frequently found in mycobacteriophages and also in phages infecting marine pelagic Actinobacteria. Its presence suggests a common and widespread strategy of modulation of host transcriptional machinery upon infection via this transcriptional switch. We present evidence that some whiB-carrying phages infect the acI lineage of Actinobacteria. At least one of them encodes the ADP-ribosylating component of the widespread bacterial AB toxins family (for example, clostridial toxin). We posit that the presence of this toxin reflects a 'trojan horse' strategy, providing protection at the population level to the abundant host microbes against eukaryotic predators.

Endophytic actinobacteria of medicinal plants: diversity and bioactivity.

PubMed

Golinska, Patrycja; Wypij, Magdalena; Agarkar, Gauravi; Rathod, Dnyaneshwar; Dahm, Hanna; Rai, Mahendra

2015-08-01

Endophytes are the microorganisms that exist inside the plant tissues without having any negative impact on the host plant. Medicinal plants constitute the huge diversity of endophytic actinobacteria of economical importance. These microbes have huge potential to synthesis of numerous novel compounds that can be exploited in pharmaceutical, agricultural and other industries. It is of prime importance to focus the present research on practical utilization of this microbial group in order to find out the solutions to the problems related to health, environment and agriculture. An extensive characterization of diverse population of endophytic actinobacteria associated with medicinal plants can provide a greater insight into the plant-endophyte interactions and evolution of mutualism. In the present review, we have discussed the diversity of endophytic actinobacteria of from medicinal plants their multiple bioactivities.

Analysis of Actinobacteria from mould-colonized water damaged building material.

PubMed

Schäfer, Jenny; Jäckel, Udo; Kämpfer, Peter

2010-08-01

Mould-colonized water damaged building materials are frequently co-colonized by actinomycetes. Here, we report the results of the analyses of Actinobacteria on different wall materials from water damaged buildings obtained by both cultivation-dependent and cultivation-independent methods. Actinobacteria were detected in all but one of the investigated materials by both methods. The detected concentrations of Actinobacteria ranged between 1.8 x 10(4) and 7.6 x 10(7) CFUg(-1) of investigated material. A total of 265 isolates from 17 materials could be assigned to 31 different genera of the class Actinobacteria on the basis of 16S rRNA gene sequence analyses. On the basis of the cultivation-independent approach, 16S rRNA gene inserts of 800 clones (50%) were assigned to 47 different genera. Representatives of the genera Streptomyces, Amycolatopsis, Nocardiopsis, Saccharopolyspora, Promicromonospora, and Pseudonocardia were found most frequently. The results derived from both methods indicated a high abundance and variety of Actinobacteria in water damaged buildings. Four bioaerosol samples were investigated by the cultivation-based approach in order to compare the communities of Actinobacteria in building material and associated air samples. A comparison of the detected genera of bioaerosol samples with those directly obtained from material samples resulted in a congruent finding of 9 of the overall 35 detected genera (25%), whereas four genera were only detected in bioaerosol samples. Copyright 2010 Elsevier GmbH. All rights reserved.

Antimicrobial Activity of Actinobacteria Isolated From the Guts of Subterranean Termites.

PubMed

Arango, R A; Carlson, C M; Currie, C R; McDonald, B R; Book, A J; Green, F; Lebow, N K; Raffa, K F

2016-12-01

Subterranean termites need to minimize potentially pathogenic and competitive fungi in their environment in order to maintain colony health. We examined the ability of Actinobacteria isolated from termite guts in suppressing microorganisms commonly encountered in a subterranean environment. Guts from two subterranean termite species, Reticulitermes flavipes (Kollar) and Reticulitermes tibialis Banks, were extracted and plated on selective chitin media. A total of 38 Actinobacteria isolates were selected for in vitro growth inhibition assays. Target microbes included three strains of Serratia marcescens Bizio, two mold fungi (Trichoderma sp. and Metarhizium sp.), a yeast fungus (Candida albicans (C.P. Robin) Berkhout), and four basidiomycete fungi (Gloeophyllum trabeum (Persoon) Murrill, Tyromyces palustris (Berkeley & M.A. Curtis) Murrill, Irpex lacteus (Fries) Fries, and Trametes versicolor (L.) Lloyd). Results showed both broad and narrow ranges of antimicrobial activity against the mold fungi, yeast fungus, and S. marcescens isolates by the Actinobacteria selected. This suggests that termite gut-associated Actinobacteria produce secondary antimicrobial compounds that may be important for pathogen inhibition in termites. Basidiomycete fungi were strongly inhibited by the selected Actinobacteria isolates, with G. trabeum and T. versicolor being most inhibited, followed by I. lacteus and T. palustris The degree of inhibition was correlated with shifts in pH caused by the Actinobacteria. Nearly all Actinobacteria isolates raised pH of the growth medium to basic levels (i.e. pH ∼8.0-9.5). We summarize antimicrobial activity of these termite gut-associated Actinobacteria and examine the implications of these pH shifts. Published by Oxford University Press on behalf of Entomological Society of America 2016. This work is written by US Government employees and is in the public domain in the US.

Mangrove rare actinobacteria: taxonomy, natural compound, and discovery of bioactivity

PubMed Central

Azman, Adzzie-Shazleen; Othman, Iekhsan; Velu, Saraswati S.; Chan, Kok-Gan; Lee, Learn-Han

2015-01-01

Actinobacteria are one of the most important and efficient groups of natural metabolite producers. The genus Streptomyces have been recognized as prolific producers of useful natural compounds as they produced more than half of the naturally-occurring antibiotics isolated to-date and continue as the primary source of new bioactive compounds. Lately, Streptomyces groups isolated from different environments produced the same types of compound, possibly due to frequent genetic exchanges between species. As a result, there is a dramatic increase in demand to look for new compounds which have pharmacological properties from another group of Actinobacteria, known as rare actinobacteria; which is isolated from special environments such as mangrove. Recently, mangrove ecosystem is becoming a hot spot for studies of bioactivities and the discovery of natural products. Many novel compounds discovered from the novel rare actinobacteria have been proven as potential new drugs in medical and pharmaceutical industries such as antibiotics, antimicrobials, antibacterials, anticancer, and antifungals. This review article highlights the latest studies on the discovery of natural compounds from the novel mangrove rare actinobacteria and provides insight on the impact of these findings. PMID:26347734

Mangrove rare actinobacteria: taxonomy, natural compound, and discovery of bioactivity.

PubMed

Azman, Adzzie-Shazleen; Othman, Iekhsan; Velu, Saraswati S; Chan, Kok-Gan; Lee, Learn-Han

2015-01-01

Actinobacteria are one of the most important and efficient groups of natural metabolite producers. The genus Streptomyces have been recognized as prolific producers of useful natural compounds as they produced more than half of the naturally-occurring antibiotics isolated to-date and continue as the primary source of new bioactive compounds. Lately, Streptomyces groups isolated from different environments produced the same types of compound, possibly due to frequent genetic exchanges between species. As a result, there is a dramatic increase in demand to look for new compounds which have pharmacological properties from another group of Actinobacteria, known as rare actinobacteria; which is isolated from special environments such as mangrove. Recently, mangrove ecosystem is becoming a hot spot for studies of bioactivities and the discovery of natural products. Many novel compounds discovered from the novel rare actinobacteria have been proven as potential new drugs in medical and pharmaceutical industries such as antibiotics, antimicrobials, antibacterials, anticancer, and antifungals. This review article highlights the latest studies on the discovery of natural compounds from the novel mangrove rare actinobacteria and provides insight on the impact of these findings.

[Isolation of actinobacteria with antibiotic associated with soft coral Nephthea sp].

PubMed

Ma, Liang; Zhang, Wenjun; Zhu, Yiguang; Wu, Zhengchao; Saurav, Kumar; Hang, Hui; Zhang, Changsheng

2013-10-04

The present study aims to isolate and identify actinobacteria associated with the soft coral Nephthea sp., and to isolate natural products from these actinobacteria under the guidance of PCR screening for polyketides synthase (PKS) genes. Eleven selective media were used to isolate actinobacteria associated with the soft coral Nephthea sp. collected from Yongxin Island. The isolated actinobacteria were classified on the basis of phylogenetic tree analysis of their 16S rRNA genes. Degenerated primers targeted on conserved KS (ketoacyl-synthase) domain of type I PKS genes were used to screen for potential isolates. The positive isolates were cultured in three different media to check their producing profiles. One bioactive strain that is rich in metabolites was subjected to larger scale fermentation for isolating bioactive natural products. A total of 20 strains were isolated from Nephthea sp., and were categorized into 3 genera including Streptomyces, Dietzia and Salinospora, among which 18 strains were positive in screening with type I PKS genes. Two bioactive compounds rifamycin S and rifamycin W were isolated and identified from Salinospora arenicola SH04. This is the first report of isolating indigenous marine actinobacteria Salinospora from the soft coral Nephthea sp. It provides an example of isolating bioactive secondary metabolites from cultivable actinobacteria associated with Nephthea sp. by PCR screening.

Plasmid-Mediated Antimicrobial Resistance in Staphylococci and Other Firmicutes.

PubMed

Schwarz, Stefan; Shen, Jianzhong; Wendlandt, Sarah; Fessler, Andrea T; Wang, Yang; Kadlec, Kristina; Wu, Cong-Ming

2014-12-01

In staphylococci and other Firmicutes, resistance to numerous classes of antimicrobial agents, which are commonly used in human and veterinary medicine, is mediated by genes that are associated with mobile genetic elements. The gene products of some of these antimicrobial resistance genes confer resistance to only specific members of a certain class of antimicrobial agents, whereas others confer resistance to the entire class or even to members of different classes of antimicrobial agents. The resistance mechanisms specified by the resistance genes fall into any of three major categories: active efflux, enzymatic inactivation, and modification/replacement/protection of the target sites of the antimicrobial agents. Among the mobile genetic elements that carry such resistance genes, plasmids play an important role as carriers of primarily plasmid-borne resistance genes, but also as vectors for nonconjugative and conjugative transposons that harbor resistance genes. Plasmids can be exchanged by horizontal gene transfer between members of the same species but also between bacteria belonging to different species and genera. Plasmids are highly flexible elements, and various mechanisms exist by which plasmids can recombine, form cointegrates, or become integrated in part or in toto into the chromosomal DNA or into other plasmids. As such, plasmids play a key role in the dissemination of antimicrobial resistance genes within the gene pool to which staphylococci and other Firmicutes have access. This chapter is intended to provide an overview of the current knowledge of plasmid-mediated antimicrobial resistance in staphylococci and other Firmicutes.

Bioactivity Assessment of Indian Origin-Mangrove Actinobacteria against Candida albicans.

PubMed

Pavan Kumar, J G S; Gomathi, Ajitha; Gothandam, K M; Vasconcelos, Vitor

2018-02-12

Actinobacteria is found to have a potent metabolic activity against pathogens. The present study reveals the assessment of potent antifungal secondary metabolites from actinobacteria isolated from Indian marine mangrove sediments. The samples were collected from the coastal regions of Muthupet, Andaman and the Nicobar Islands. Identification was carried out using 16S rRNA analysis and biosynthetic genes (Polyketide synthase type I/II and Non-ribosomal peptide synthase) were screened. Actinobacteria were assayed for their antifungal activity against 16 clinical Candida albicans and the compound analysis was performed using gas chromatography-mass spectrometry GC-MS. The 31 actinobacterial strains were isolated and 16S rRNA gene sequencing revealed that this ecosystem is rich on actinobacteria, with Streptomyces as the predominant genus. The PCR based screening of biosynthetic genes revealed the presence of PKS-I in six strains, PKS-II in four strains and NRPS in 11 strains. The isolated actinobacteria VITGAP240 and VITGAP241 (two isolates) were found to have a potential antifungal activity against all the tested C. albicans . GC-MS results revealed that the actinobacterial compounds were belonging to heterocyclic, polyketides and peptides. Overall, the strains possess a wide spectrum of antifungal properties which affords the production of significant bioactive metabolites as potential antibiotics.

Bioactivity Assessment of Indian Origin—Mangrove Actinobacteria against Candida albicans

PubMed Central

Pavan Kumar, J. G. S.; Gomathi, Ajitha; Vasconcelos, Vitor

2018-01-01

Actinobacteria is found to have a potent metabolic activity against pathogens. The present study reveals the assessment of potent antifungal secondary metabolites from actinobacteria isolated from Indian marine mangrove sediments. The samples were collected from the coastal regions of Muthupet, Andaman and the Nicobar Islands. Identification was carried out using 16S rRNA analysis and biosynthetic genes (Polyketide synthase type I/II and Non-ribosomal peptide synthase) were screened. Actinobacteria were assayed for their antifungal activity against 16 clinical Candida albicans and the compound analysis was performed using gas chromatography-mass spectrometry GC-MS. The 31 actinobacterial strains were isolated and 16S rRNA gene sequencing revealed that this ecosystem is rich on actinobacteria, with Streptomyces as the predominant genus. The PCR based screening of biosynthetic genes revealed the presence of PKS-I in six strains, PKS-II in four strains and NRPS in 11 strains. The isolated actinobacteria VITGAP240 and VITGAP241 (two isolates) were found to have a potential antifungal activity against all the tested C. albicans. GC-MS results revealed that the actinobacterial compounds were belonging to heterocyclic, polyketides and peptides. Overall, the strains possess a wide spectrum of antifungal properties which affords the production of significant bioactive metabolites as potential antibiotics. PMID:29439535

Response of microbial community of organic-matter-impoverished arable soil to long-term application of soil conditioner derived from dynamic rapid fermentation of food waste

PubMed Central

Hou, Jiaqi; Li, Mingxiao; Mao, Xuhui; Hao, Yan; Ding, Jie; Liu, Dongming; Liu, Hongliang

2017-01-01

Rapid fermentation of food waste can be used to prepare soil conditioner. This process consumes less time and is more cost-effective than traditional preparation technology. However, the succession of the soil microbial community structure after long-term application of rapid fermentation-derived soil conditioners remains unclear. Herein, dynamic rapid fermentation (DRF) of food waste was performed to develop a soil conditioner and the successions and diversity of bacterial communities in an organic-matter-impoverished arable soil after six years of application of DRF-derived soil conditioner were investigated. Results showed that the treatment increased soil organic matter (SOM) accumulation and strawberry yield by 5.3 g/kg and 555.91 kg/ha, respectively. Proteobacteria, Actinobacteria, Acidobacteria, and Firmicutes became the dominant phyla, occupying 65.95%–77.52% of the bacterial sequences. Principal component analysis (PCA) results showed that the soil bacterial communities were largely influenced by the treatment. Redundancy analysis (RDA) results showed that the relative abundances of Gemmatimonadetes, Chloroflexi, Verrucomicrobia, Nitrospirae, and Firmicutes were significantly correlated with soil TC, TN, TP, NH4+-N, NO3−-N, OM, and moisture. These communities were all distributed in the soil samples collected in the sixth year of application. Long-term treatment did not enhance the diversity of bacterial species but significantly altered the distribution of major functional bacterial communities in the soils. Application of DRF-derived soil conditioner could improve the soil quality and optimize the microbial community, ultimately enhancing fruit yields. PMID:28419163

Response of microbial community of organic-matter-impoverished arable soil to long-term application of soil conditioner derived from dynamic rapid fermentation of food waste.

PubMed

Hou, Jiaqi; Li, Mingxiao; Mao, Xuhui; Hao, Yan; Ding, Jie; Liu, Dongming; Xi, Beidou; Liu, Hongliang

2017-01-01

Rapid fermentation of food waste can be used to prepare soil conditioner. This process consumes less time and is more cost-effective than traditional preparation technology. However, the succession of the soil microbial community structure after long-term application of rapid fermentation-derived soil conditioners remains unclear. Herein, dynamic rapid fermentation (DRF) of food waste was performed to develop a soil conditioner and the successions and diversity of bacterial communities in an organic-matter-impoverished arable soil after six years of application of DRF-derived soil conditioner were investigated. Results showed that the treatment increased soil organic matter (SOM) accumulation and strawberry yield by 5.3 g/kg and 555.91 kg/ha, respectively. Proteobacteria, Actinobacteria, Acidobacteria, and Firmicutes became the dominant phyla, occupying 65.95%-77.52% of the bacterial sequences. Principal component analysis (PCA) results showed that the soil bacterial communities were largely influenced by the treatment. Redundancy analysis (RDA) results showed that the relative abundances of Gemmatimonadetes, Chloroflexi, Verrucomicrobia, Nitrospirae, and Firmicutes were significantly correlated with soil TC, TN, TP, NH4+-N, NO3--N, OM, and moisture. These communities were all distributed in the soil samples collected in the sixth year of application. Long-term treatment did not enhance the diversity of bacterial species but significantly altered the distribution of major functional bacterial communities in the soils. Application of DRF-derived soil conditioner could improve the soil quality and optimize the microbial community, ultimately enhancing fruit yields.

Marine actinobacteria associated with marine organisms and their potentials in producing pharmaceutical natural products.

PubMed

Valliappan, Karuppiah; Sun, Wei; Li, Zhiyong

2014-09-01

Actinobacteria are ubiquitous in the marine environment, playing an important ecological role in the recycling of refractory biomaterials and producing novel natural products with pharmic applications. Actinobacteria have been detected or isolated from the marine creatures such as sponges, corals, mollusks, ascidians, seaweeds, and seagrass. Marine organism-associated actinobacterial 16S rRNA gene sequences, i.e., 3,003 sequences, deposited in the NCBI database clearly revealed enormous numbers of actinobacteria associated with marine organisms. For example, RDP classification of these sequences showed that 112 and 62 actinobacterial genera were associated with the sponges and corals, respectively. In most cases, it is expected that these actinobacteria protect the host against pathogens by producing bioactive compounds. Natural products investigation and functional gene screening of the actinobacteria associated with the marine organisms revealed that they can synthesize numerous natural products including polyketides, isoprenoids, phenazines, peptides, indolocarbazoles, sterols, and others. These compounds showed anticancer, antimicrobial, antiparasitic, neurological, antioxidant, and anti-HIV activities. Therefore, marine organism-associated actinobacteria represent an important resource for marine drugs. It is an upcoming field of research to search for novel actinobacteria and pharmaceutical natural products from actinobacteria associated with the marine organisms. In this review, we attempt to summarize the present knowledge on the diversity and natural products production of actinobacteria associated with the marine organisms, based on the publications from 1991 to 2013.

Evolution and Ecology of Actinobacteria and Their Bioenergy Applications

PubMed Central

Lewin, Gina R.; Carlos, Camila; Chevrette, Marc G.; Horn, Heidi A.; McDonald, Bradon R.; Stankey, Robert J.; Fox, Brian G.; Currie, Cameron R.

2017-01-01

The ancient phylum Actinobacteria is composed of phylogenetically and physiologically diverse bacteria that help Earth’s ecosystems function. As free-living organisms and symbionts of herbivorous animals, Actinobacteria contribute to the global carbon cycle through the breakdown of plant biomass. In addition, they mediate community dynamics as producers of small molecules with diverse biological activities. Together, the evolution of high cellulolytic ability and diverse chemistry, shaped by their ecological roles in nature, make Actinobacteria a promising group for the bioenergy industry. Specifically, their enzymes can contribute to industrial-scale breakdown of cellulosic plant biomass into simple sugars that can then be converted into biofuels. Furthermore, harnessing their ability to biosynthesize a range of small molecules has potential for the production of specialty biofuels. PMID:27607553

Evolution and Ecology of Actinobacteria and Their Bioenergy Applications.

PubMed

Lewin, Gina R; Carlos, Camila; Chevrette, Marc G; Horn, Heidi A; McDonald, Bradon R; Stankey, Robert J; Fox, Brian G; Currie, Cameron R

2016-09-08

The ancient phylum Actinobacteria is composed of phylogenetically and physiologically diverse bacteria that help Earth's ecosystems function. As free-living organisms and symbionts of herbivorous animals, Actinobacteria contribute to the global carbon cycle through the breakdown of plant biomass. In addition, they mediate community dynamics as producers of small molecules with diverse biological activities. Together, the evolution of high cellulolytic ability and diverse chemistry, shaped by their ecological roles in nature, make Actinobacteria a promising group for the bioenergy industry. Specifically, their enzymes can contribute to industrial-scale breakdown of cellulosic plant biomass into simple sugars that can then be converted into biofuels. Furthermore, harnessing their ability to biosynthesize a range of small molecules has potential for the production of specialty biofuels.

[Actinobacteria and their odor-producing capacities in a surface water in Shanghai].

PubMed

Chen, Jiao; Bai, Xiao-hui; Lu, Ning; Wang, Xian-yun; Zhang, Yong-hui; Wu, Pan-cheng; Guo, Xin-chi

2014-10-01

The odor in raw water is one of the main sources of odor in drinking water. The occurrence of actinobacteria and their odor producing capacities in a reservoir in.Shanghai were investigated. Gauze's medium and membrane filtration were used for actinobacteria isolation. Through combined methods of 16S rRNA sequencing, colony and hyphae morphology, carbon source utilization, physiological and biochemical characteristics, 40 strains of actinobacteria were identified from the reservoir. Results showed that there were 38 Streptomyces, an Aeromicrobium and a Pseudonocardia. Liquid culture medium and the real reservoir water were used to test the odor producing capacity of these 40 strains of actinobacteria, and headspace solid phase microextraction (HS-SPME) and high resolution gas chromatography mass spectroscopy (GC/MS) were used to analyze the odor compounds 2-methylisoborneol (2-MIB) and geosmin (GSM) in the fermentation liquor. The test results showed that, the odor-producing capacities of these actinobacteria in different fermentation media showed different variation trends, even within the genera Streptomyces. The odor-producing capacity of actinobacteria in the liquid culture medium could not represent their states in the reservoir water or their actual odor contribution to the aquatic environment.

Groundwater Chemistry and Microbial Ecology Effects on Explosives Biodegradation

DTIC Science & Technology

2008-09-01

was detected (grouping near the known RDX-degrading actinobacteria ). Two bands recovered from RDX- degrading groundwater amended with succinate...about equal numbers of genera in the betaproteobacteria, gammaproteobacteria, actinobacteria , and firmicutes phyla. 3) The lack of detection of...microorganisms capable of using RDX as a nitrogen source) of 8 microcosms receiving cheese whey. The 16S rRNA gene sequences belonged to Actinobacteria 9

Exploring the potential for actinobacteria as defensive symbionts in fungus-growing termites.

PubMed

Visser, Anna A; Nobre, Tânia; Currie, Cameron R; Aanen, Duur K; Poulsen, Michael

2012-05-01

In fungus-growing termites, fungi of the subgenus Pseudoxylaria threaten colony health through substrate competition with the termite fungus (Termitomyces). The potential mechanisms with which termites suppress Pseudoxylaria have remained unknown. Here we explore if Actinobacteria potentially play a role as defensive symbionts against Pseudoxylaria in fungus-growing termites. We sampled for Actinobacteria from 30 fungus-growing termite colonies, spanning the three main termite genera and two geographically distant sites. Our isolations yielded 360 Actinobacteria, from which we selected subsets for morphological (288 isolates, grouped in 44 morphotypes) and for 16S rRNA (35 isolates, spanning the majority of morphotypes) characterisation. Actinobacteria were found throughout all sampled nests and colony parts and, phylogenetically, they are interspersed with Actinobacteria from origins other than fungus-growing termites, indicating lack of specificity. Antibiotic-activity screening of 288 isolates against the fungal cultivar and competitor revealed that most of the Actinobacteria-produced molecules with antifungal activity. A more detailed bioassay on 53 isolates, to test the specificity of antibiotics, showed that many Actinobacteria inhibit both Pseudoxylaria and Termitomyces, and that the cultivar fungus generally is more susceptible to inhibition than the competitor. This suggests that either defensive symbionts are not present in the system or that they, if present, represent a subset of the community isolated. If so, the antibiotics must be used in a targeted fashion, being applied to specific areas by the termites. We describe the first discovery of an assembly of antibiotic-producing Actinobacteria occurring in fungus-growing termite nests. However, due to the diversity found, and the lack of both phylogenetic and bioactivity specificity, further work is necessary for a better understanding of the putative role of antibiotic-producing bacteria in the fungus

Successful enrichment of the ubiquitous freshwater acI Actinobacteria.

PubMed

Garcia, Sarahi L; McMahon, Katherine D; Grossart, Hans-Peter; Warnecke, Falk

2014-02-01

Actinobacteria of the acI lineage are often the numerically dominant bacterial phylum in surface freshwaters, where they can account for > 50% of total bacteria. Despite their abundance, there are no described isolates. In an effort to obtain enrichment of these ubiquitous freshwater Actinobacteria, diluted freshwater samples from Lake Grosse Fuchskuhle, Germany, were incubated in 96-well culture plates. With this method, a successful enrichment containing high abundances of a member of the lineage acI was established. Phylogenetic classification showed that the acI Actinobacteria of the enrichment belonged to the acI-B2 tribe, which seems to prefer acidic lakes. This enrichment grows to low cell densities and thus the oligotrophic nature of acI-B2 was confirmed. © 2013 Society for Applied Microbiology and John Wiley & Sons Ltd.

Impact of long-term cropping of glyphosate-resistant transgenic soybean [Glycine max (L.) Merr.] on soil microbiome.

PubMed

Babujia, Letícia Carlos; Silva, Adriana Pereira; Nakatani, André Shigueyoshi; Cantão, Mauricio Egidio; Vasconcelos, Ana Tereza Ribeiro; Visentainer, Jesuí Vergilio; Hungria, Mariangela

2016-08-01

The transgenic soybean [Glycine max (L.) Merrill] occupies about 80 % of the global area cropped with this legume, the majority comprising the glyphosate-resistant trait (Roundup Ready(®), GR or RR). However, concerns about possible impacts of transgenic crops on soil microbial communities are often raised. We investigated soil chemical, physical and microbiological properties, and grain yields in long-term field trials involving conventional and nearly isogenic RR transgenic genotypes. The trials were performed at two locations in Brazil, with different edaphoclimatic conditions. Large differences in physical, chemical and classic microbiological parameters (microbial biomass of C and N, basal respiration), as well as in grain production were observed between the sites. Some phyla (Proteobacteria, Actinobacteria, Acidobacteria), classes (Alphaproteobacteria, Actinomycetales, Solibacteres) and orders (Rhizobiales, Burkholderiales, Myxococcales, Pseudomonadales), as well as some functional subsystems (clustering-based subsystems, carbohydrates, amino acids and protein metabolism) were, in general, abundant in all treatments. However, bioindicators related to superior soil fertility and physical properties at Londrina were identified, among them a higher ratio of Proteobacteria:Acidobacteria. Regarding the transgene, the metagenomics showed differences in microbial taxonomic and functional abundances, but lower in magnitude than differences observed between the sites. Besides the site-specific differences, Proteobacteria, Firmicutes and Chlorophyta were higher in the transgenic treatment, as well as sequences related to protein metabolism, cell division and cycle. Although confirming effects of the transgenic trait on soil microbiome, no differences were recorded in grain yields, probably due to the buffering capacity associated with the high taxonomic and functional microbial diversity observed in all treatments.

Effect of Sugarcane Burning or Green Harvest Methods on the Brazilian Cerrado Soil Bacterial Community Structure

PubMed Central

Rachid, Caio T. C. C.; Santos, Adriana L.; Piccolo, Marisa C.; Balieiro, Fabiano C.; Coutinho, Heitor L. C.; Peixoto, Raquel S.; Tiedje, James M.; Rosado, Alexandre S.

2013-01-01

Background The Brazilian Cerrado is one of the most important biodiversity reservoirs in the world. The sugarcane cultivation is expanding in this biome and necessitates the study of how it may impact the soil properties of the Cerrado. There is a lack of information especially about the impacts of different sugarcane management on the native bacterial communities of Cerrado soil. Therefore, our objective was to evaluate and compare the soil bacterial community structure of the Cerrado vegetation with two sugarcane systems. Methods We evaluated samples under native vegetation and the impact of the two most commonly used management strategies for sugarcane cultivation (burnt cane and green cane) on this diversity using pyrosequencing and quantitative PCR of the rrs gene (16S rRNA). Results and Conclusions Nineteen different phyla were identified, with Acidobacteria (≈35%), Proteobacteria (≈24%) and Actinobacteria (≈21%) being the most abundant. Many of the sequences were represented by few operational taxonomic units (OTUs, 3% of dissimilarity), which were found in all treatments. In contrast, there were very strong patterns of local selection, with many OTUs occurring only in one sample. Our results reveal a complex bacterial diversity, with a large fraction of microorganisms not yet described, reinforcing the importance of this biome. As possible sign of threat, the qPCR detected a reduction of the bacterial population in agricultural soils compared with native Cerrado soil communities. We conclude that sugarcane cultivation promoted significant structural changes in the soil bacterial community, with Firmicutes phylum and Acidobacteria classes being the groups most affected. PMID:23533619

Effect of sugarcane burning or green harvest methods on the Brazilian Cerrado soil bacterial community structure.

PubMed

Rachid, Caio T C C; Santos, Adriana L; Piccolo, Marisa C; Balieiro, Fabiano C; Coutinho, Heitor L C; Peixoto, Raquel S; Tiedje, James M; Rosado, Alexandre S

2013-01-01

The Brazilian Cerrado is one of the most important biodiversity reservoirs in the world. The sugarcane cultivation is expanding in this biome and necessitates the study of how it may impact the soil properties of the Cerrado. There is a lack of information especially about the impacts of different sugarcane management on the native bacterial communities of Cerrado soil. Therefore, our objective was to evaluate and compare the soil bacterial community structure of the Cerrado vegetation with two sugarcane systems. We evaluated samples under native vegetation and the impact of the two most commonly used management strategies for sugarcane cultivation (burnt cane and green cane) on this diversity using pyrosequencing and quantitative PCR of the rrs gene (16S rRNA). Nineteen different phyla were identified, with Acidobacteria (≈35%), Proteobacteria (≈24%) and Actinobacteria (≈21%) being the most abundant. Many of the sequences were represented by few operational taxonomic units (OTUs, 3% of dissimilarity), which were found in all treatments. In contrast, there were very strong patterns of local selection, with many OTUs occurring only in one sample. Our results reveal a complex bacterial diversity, with a large fraction of microorganisms not yet described, reinforcing the importance of this biome. As possible sign of threat, the qPCR detected a reduction of the bacterial population in agricultural soils compared with native Cerrado soil communities. We conclude that sugarcane cultivation promoted significant structural changes in the soil bacterial community, with Firmicutes phylum and Acidobacteria classes being the groups most affected.

Phylogenetic Framework and Molecular Signatures for the Main Clades of the Phylum Actinobacteria

PubMed Central

Gao, Beile

2012-01-01

Summary: The phylum Actinobacteria harbors many important human pathogens and also provides one of the richest sources of natural products, including numerous antibiotics and other compounds of biotechnological interest. Thus, a reliable phylogeny of this large phylum and the means to accurately identify its different constituent groups are of much interest. Detailed phylogenetic and comparative analyses of >150 actinobacterial genomes reported here form the basis for achieving these objectives. In phylogenetic trees based upon 35 conserved proteins, most of the main groups of Actinobacteria as well as a number of their superageneric clades are resolved. We also describe large numbers of molecular markers consisting of conserved signature indels in protein sequences and whole proteins that are specific for either all Actinobacteria or their different clades (viz., orders, families, genera, and subgenera) at various taxonomic levels. These signatures independently support the existence of different phylogenetic clades, and based upon them, it is now possible to delimit the phylum Actinobacteria (excluding Coriobacteriia) and most of its major groups in clear molecular terms. The species distribution patterns of these markers also provide important information regarding the interrelationships among different main orders of Actinobacteria. The identified molecular markers, in addition to enabling the development of a stable and reliable phylogenetic framework for this phylum, also provide novel and powerful means for the identification of different groups of Actinobacteria in diverse environments. Genetic and biochemical studies on these Actinobacteria-specific markers should lead to the discovery of novel biochemical and/or other properties that are unique to different groups of Actinobacteria. PMID:22390973

Parallel Evolution and Horizontal Gene Transfer of the pst Operon in Firmicutes from Oligotrophic Environments

PubMed Central

Moreno-Letelier, Alejandra; Olmedo, Gabriela; Eguiarte, Luis E.; Martinez-Castilla, Leon; Souza, Valeria

2011-01-01

The high affinity phosphate transport system (pst) is crucial for phosphate uptake in oligotrophic environments. Cuatro Cienegas Basin (CCB) has extremely low P levels and its endemic Bacillus are closely related to oligotrophic marine Firmicutes. Thus, we expected the pst operon of CCB to share the same evolutionary history and protein similarity to marine Firmicutes. Orthologs of the pst operon were searched in 55 genomes of Firmicutes and 13 outgroups. Phylogenetic reconstructions were performed for the pst operon and 14 concatenated housekeeping genes using maximum likelihood methods. Conserved domains and 3D structures of the phosphate-binding protein (PstS) were also analyzed. The pst operon of Firmicutes shows two highly divergent clades with no correlation to the type of habitat nor a phylogenetic congruence, suggesting horizontal gene transfer. Despite sequence divergence, the PstS protein had a similar 3D structure, which could be due to parallel evolution after horizontal gene transfer events. PMID:21461370

Actinobacteria: Current research and perspectives for bioremediation of pesticides and heavy metals.

PubMed

Alvarez, Analia; Saez, Juliana Maria; Davila Costa, José Sebastian; Colin, Veronica Leticia; Fuentes, María Soledad; Cuozzo, Sergio Antonio; Benimeli, Claudia Susana; Polti, Marta Alejandra; Amoroso, María Julia

2017-01-01

Actinobacteria exhibit cosmopolitan distribution since their members are widely distributed in aquatic and terrestrial ecosystems. In the environment they play relevant ecological roles including recycling of substances, degradation of complex polymers, and production of bioactive molecules. Biotechnological potential of actinobacteria in the environment was demonstrated by their ability to remove organic and inorganic pollutants. This ability is the reason why actinobacteria have received special attention as candidates for bioremediation, which has gained importance because of the widespread release of contaminants into the environment. Among organic contaminants, pesticides are widely used for pest control, although the negative impact of these chemicals in the environmental balance is increasingly becoming apparent. Similarly, the extensive application of heavy metals in industrial processes lead to highly contaminated areas worldwide. Several studies focused in the use of actinobacteria for cleaning up the environment were performed in the last 15 years. Strategies such as bioaugmentation, biostimulation, cell immobilization, production of biosurfactants, design of defined mixed cultures and the use of plant-microbe systems were developed to enhance the capabilities of actinobacteria in bioremediation. In this review, we compiled and discussed works focused in the study of different bioremediation strategies using actinobacteria and how they contributed to the improvement of the already existing strategies. In addition, we discuss the importance of omic studies to elucidate mechanisms and regulations that bacteria use to cope with pollutant toxicity, since they are still little known in actinobacteria. A brief account of sources and harmful effects of pesticides and heavy metals is also given. Copyright © 2016 Elsevier Ltd. All rights reserved.

Discovery of a new family of relaxases in Firmicutes bacteria.

PubMed

Ramachandran, Gayetri; Miguel-Arribas, Andrés; Abia, David; Singh, Praveen K; Crespo, Isidro; Gago-Córdoba, César; Hao, Jian An; Luque-Ortega, Juan Roman; Alfonso, Carlos; Wu, Ling J; Boer, D Roeland; Meijer, Wilfried J J

2017-02-01

Antibiotic resistance is a serious global problem. Antibiotic resistance genes (ARG), which are widespread in environmental bacteria, can be transferred to pathogenic bacteria via horizontal gene transfer (HGT). Gut microbiomes are especially apt for the emergence and dissemination of ARG. Conjugation is the HGT route that is predominantly responsible for the spread of ARG. Little is known about conjugative elements of Gram-positive bacteria, including those of the phylum Firmicutes, which are abundantly present in gut microbiomes. A critical step in the conjugation process is the relaxase-mediated site- and strand-specific nick in the oriT region of the conjugative element. This generates a single-stranded DNA molecule that is transferred from the donor to the recipient cell via a connecting channel. Here we identified and characterized the relaxosome components oriT and the relaxase of the conjugative plasmid pLS20 of the Firmicute Bacillus subtilis. We show that the relaxase gene, named relLS20, is essential for conjugation, that it can function in trans and provide evidence that Tyr26 constitutes the active site residue. In vivo and in vitro analyses revealed that the oriT is located far upstream of the relaxase gene and that the nick site within oriT is located on the template strand of the conjugation genes. Surprisingly, the RelLS20 shows very limited similarity to known relaxases. However, more than 800 genes to which no function had been attributed so far are predicted to encode proteins showing significant similarity to RelLS20. Interestingly, these putative relaxases are encoded almost exclusively in Firmicutes bacteria. Thus, RelLS20 constitutes the prototype of a new family of relaxases. The identification of this novel relaxase family will have an important impact in different aspects of future research in the field of HGT in Gram-positive bacteria in general, and specifically in the phylum of Firmicutes, and in gut microbiome research.

Discovery of a new family of relaxases in Firmicutes bacteria

PubMed Central

Singh, Praveen K.; Hao, Jian An; Luque-Ortega, Juan Roman; Wu, Ling J.; Boer, D. Roeland

2017-01-01

Antibiotic resistance is a serious global problem. Antibiotic resistance genes (ARG), which are widespread in environmental bacteria, can be transferred to pathogenic bacteria via horizontal gene transfer (HGT). Gut microbiomes are especially apt for the emergence and dissemination of ARG. Conjugation is the HGT route that is predominantly responsible for the spread of ARG. Little is known about conjugative elements of Gram-positive bacteria, including those of the phylum Firmicutes, which are abundantly present in gut microbiomes. A critical step in the conjugation process is the relaxase-mediated site- and strand-specific nick in the oriT region of the conjugative element. This generates a single-stranded DNA molecule that is transferred from the donor to the recipient cell via a connecting channel. Here we identified and characterized the relaxosome components oriT and the relaxase of the conjugative plasmid pLS20 of the Firmicute Bacillus subtilis. We show that the relaxase gene, named relLS20, is essential for conjugation, that it can function in trans and provide evidence that Tyr26 constitutes the active site residue. In vivo and in vitro analyses revealed that the oriT is located far upstream of the relaxase gene and that the nick site within oriT is located on the template strand of the conjugation genes. Surprisingly, the RelLS20 shows very limited similarity to known relaxases. However, more than 800 genes to which no function had been attributed so far are predicted to encode proteins showing significant similarity to RelLS20. Interestingly, these putative relaxases are encoded almost exclusively in Firmicutes bacteria. Thus, RelLS20 constitutes the prototype of a new family of relaxases. The identification of this novel relaxase family will have an important impact in different aspects of future research in the field of HGT in Gram-positive bacteria in general, and specifically in the phylum of Firmicutes, and in gut microbiome research. PMID:28207825

Microbial community analysis of an Alabama coastal salt marsh impacted by the Deepwater Horizon Oil Spill

NASA Astrophysics Data System (ADS)

Beazley, M. J.; Martinez, R.; Rajan, S.; Powell, J.; Piceno, Y.; Tom, L.; Andersen, G. L.; Hazen, T. C.; Van Nostrand, J. D.; Zhou, J.; Mortazavi, B.; Sobecky, P. A.

2011-12-01

Microbial community responses of an Alabama coastal salt marsh environment to the Deepwater Horizon oil spill were studied by 16S rRNA (PhyloChip) and functional gene (GeoChip) microarray-based analysis. Oil and tar balls associated with the oil spill arrived along the Alabama coast in June 2010. Marsh and inlet sediment samples collected in June, July, and September 2010 from a salt marsh ecosystem at Point Aux Pines Alabama were analyzed to determine if bacterial community structure changed as a result of oil perturbation. Sediment total petroleum hydrocarbon (TPH) concentrations ranged from below detection to 189 mg kg-1 and were randomly dispersed throughout the salt marsh sediments. Total DNA extracted from sediment and particulates were used for PhyloChip and GeoChip hybridization. A total of 4000 to 8000 operational taxonomic units (OTUs) were detected in marsh and inlet samples. Distinctive changes in the number of detectable OTUs were observed between June, July, and September 2010. Surficial inlet sediments demonstrated a significant increase in the total number of OTUs between June and September that correlated with TPH concentrations. The most significant increases in bacterial abundance were observed in the phyla Actinobacteria, Firmicutes, Gemmatimonadetes, Proteobacteria, and Verrucomicrobia. Bacterial richness in marsh sediments also correlated with TPH concentrations with significant changes primarily in Acidobacteria, Actinobacteria, Firmicutes, Fusobacteria, Nitrospirae, and Proteobacteria. GeoChip microarray analysis detected 5000 to 8300 functional genes in marsh and inlet samples. Surficial inlet sediments demonstrated distinctive increases in the number of detectable genes and gene signal intensities in July samples compared to June. Signal intensities increased (> 1.5-fold) in genes associated with petroleum degradation. Genes related to metal resistance, stress, and carbon cycling also demonstrated increases in oiled sediments. This study

Biotechnological application and taxonomical distribution of plant growth promoting actinobacteria.

PubMed

Hamedi, Javad; Mohammadipanah, Fatemeh

2015-02-01

Plant growth promoting (PGP) bacteria are involved in various interactions known to affect plant fitness and soil quality, thereby increasing the productivity of agriculture and stability of soil. Although the potential of actinobacteria in antibiotic production is well-investigated, their capacity to enhance plant growth is not fully surveyed. Due to the following justifications, PGP actinobacteria (PGPA) can be considered as a more promising taxonomical group of PGP bacteria: (1) high numbers of actinobacteria per gram of soil and their filamentous nature, (2) genome dedicated to the secondary metabolite production (~5 to 10 %) is distinctively more than that of other bacteria and (3) number of plant growth promoter genera reported from actinobacteria is 1.3 times higher than that of other bacteria. Mechanisms by which PGPA contribute to the plant growth by association are: (a) enhancing nutrients availability, (b) regulation of plant metabolism, (c) decreasing environmental stress, (d) control of phytopathogens and (e) improvement of soil texture. Taxonomical and chemical diversity of PGPA and their biotechnological application along with their associated challenges are summarized in this paper.

Effect of actinobacteria agent inoculation methods on cellulose degradation during composting based on redundancy analysis.

PubMed

Zhao, Yue; Lu, Qian; Wei, Yuquan; Cui, Hongyang; Zhang, Xu; Wang, Xueqin; Shan, Si; Wei, Zimin

2016-11-01

In this study, actinobacteria agent including Streptomyces sp. and Micromonospora sp. were inoculated during chicken manure composting by different inoculation methods. The effect of different treatments on cellulose degradation and the relationship between inoculants and indigenous actinobacteria were investigated during composting. The results showed that inoculation in different stages of composting all improved the actinobacteria community diversity particularly in the cooling stage of composting (M3). Moreover, inoculation could distinctly accelerate the degradation of organic matters (OM) especially celluloses. Redundancy analysis indicated that the correlation between indigenous actinobacteria and degradation of OM and cellulose were regulated by inoculants and there were significant differences between different inoculation methods. Furthermore, synergy between indigenous actinobacteria and inoculants for degradation of OM and cellulose in M3 was better than other treatments. Conclusively, we suggested an inoculation method to regulate the indigenous actinobacteria based on the relationship between inoculants and indigenous actinobacteria and degradation content. Copyright © 2016 Elsevier Ltd. All rights reserved.

Characterization of actinobacteria associated with three ant-plant mutualisms.

PubMed

Hanshew, Alissa S; McDonald, Bradon R; Díaz Díaz, Carol; Djiéto-Lordon, Champlain; Blatrix, Rumsaïs; Currie, Cameron R

2015-01-01

Ant-plant mutualisms are conspicuous and ecologically important components of tropical ecosystems that remain largely unexplored in terms of insect-associated microbial communities. Recent work has revealed that ants in some ant-plant systems cultivate fungi (Chaetothyriales) within their domatia, which are fed to larvae. Using Pseudomyrmex penetrator/Tachigali sp. from French Guiana and Petalomyrmex phylax/Leonardoxa africana and Crematogaster margaritae/Keetia hispida, both from Cameroon, as models, we tested the hypothesis that ant-plant-fungus mutualisms co-occur with culturable Actinobacteria. Using selective media, we isolated 861 putative Actinobacteria from the three systems. All C. margaritae/K. hispida samples had culturable Actinobacteria with a mean of 10.0 colony forming units (CFUs) per sample, while 26 % of P. penetrator/Tachigali samples (mean CFUs 1.3) and 67 % of P. phylax/L. africana samples (mean CFUs 3.6) yielded Actinobacteria. The largest number of CFUs was obtained from P. penetrator workers, P. phylax alates, and C. margaritae pupae. 16S rRNA gene sequencing and phylogenetic analysis revealed the presence of four main clades of Streptomyces and one clade of Nocardioides within these three ant-plant mutualisms. Streptomyces with antifungal properties were isolated from all three systems, suggesting that they could serve as protective symbionts, as found in other insects. In addition, a number of isolates from a clade of Streptomyces associated with P. phylax/L. africana and C. margaritae/K. hispida were capable of degrading cellulose, suggesting that Streptomyces in these systems may serve a nutritional role. Repeated isolation of particular clades of Actinobacteria from two geographically distant locations supports these isolates as residents in ant-plant-fungi niches.

Biogenesis of [Fe-S] cluster in Firmicutes: an unexploited field of investigation.

PubMed

Riboldi, Gustavo Pelicioli; de Mattos, Eduardo Preusser; Frazzon, Jeverson

2013-09-01

Iron-sulfur clusters (ISC) ([Fe-S]) are evolutionarily ancient and ubiquitous inorganic prosthetic groups present in almost all living organisms, whose biosynthetic assembly is dependent on complex protein machineries. [Fe-S] clusters are involved in biologically important processes, ranging from electron transfer catalysis to transcriptional regulatory roles. Three different systems involved in [Fe-S] cluster assembly have already been characterized in Proteobacteria, namely, the nitrogen fixation system, the ISC system and the sulfur assimilation system. Although they are well described in various microorganisms, these machineries are poorly characterized in members of the Firmicutes phylum, to which several groups of pathogenic bacteria belong. Recently, several research groups have made efforts to elucidate the biogenesis of [Fe-S] clusters at the molecular level in Firmicutes, and many important characteristics have been described. Considering the pivotal role of [Fe-S] clusters in a number of biological processes, the review presented here focuses on the description of the biosynthetic machineries for [Fe-S] cluster biogenesis in prokaryotes, followed by a discussion on recent results observed for Firmicutes [Fe-S] cluster assembly.

In-vitro antimicrobial activity of marine actinobacteria against multidrug resistance Staphylococcus aureus.

PubMed

Sathish, Kumar S R; Kokati, Venkata Bhaskara Rao

2012-10-01

To investigate the antibacterial activity of marine actinobacteria against multidrug resistance Staphylococcus aureus (MDRSA). Fifty one actinobacterial strains were isolated from salt pans soil, costal area in Kothapattanam, Ongole, Andhra Pradesh. Primary screening was done using cross-streak method against MDRSA. The bioactive compounds are extracted from efficient actinobacteria using solvent extraction. The antimicrobial activity of crude and solvent extracts was performed using Kirby-Bauer method. MIC for ethyl acetate extract was determined by modified agar well diffusion method. The potent actinobacteria are identified using Nonomura key, Shirling and Gottlieb 1966 with Bergey's manual of determinative bacteriology. Among the fifty one isolates screened for antibacterial activity, SRB25 were found efficient against MDRSA. The ethyl acetate extracts showed high inhibition against test organism. MIC test was performed with the ethyl acetate extract against MDRSA and found to be 1 000 µg/mL. The isolated actinobacteria are identified as Streptomyces sp with the help of Nonomura key. The current investigation reveals that the marine actinobacteria from salt pan environment can be able to produce new drug molecules against drug resistant microorganisms.

[Isolation methods and diversity of culturable fecal actinobacteria associated with Panthera tigris tigris in Yunnan Safari Park].

PubMed

Cao, Yanru; Jiang, Yi; Li, Youlong; Chen, Xiu; Jin, Rongxian; He, Wenxiang

2012-07-04

We studied the isolation methods and diversity of culturable fecal actinobacteria associated with Panthera tigris tigris by using culture-dependent approaches. Fresh fecal samples of healthy Panthera tigris tigris were collected from Yunnan Safari Park. Pretreatment of the samples, isolation media and inhibitors were tested for actinobacteria isolation. 16S rRNA genes of actinobacteria were sequenced and subjected to phylogenetic analysis. The abundance of culturable actinobacteria was 1.10 x 10(8) cfu/g colony forming units (CFU) per gram of feces (wet weight). We obtained 110 purified cultural actinobacterium strains. The analysis based on 16S rRNA gene sequences showed that these strains were distributed in 10 different families and 12 genera of actinobacteria at least, and most of them were non-filamentous, such as Arthrobacter, Dietzia, Kocuria, Corynebacterium and Microbacterium. Streptomyces was the mainly classical filamentous actinobacteria, and up to 64% of total. Drying and heating up the fecal samples can greatly increase the rate of the actinobacteria. Many kinds of inhibitors and chemical defined media are suitable for isolation of fecal actinobacteria. The culturable actinobacteria are abundant in Panthera tigris tigris feces. Our study found an effective method to isolate animals' fecal actinobacteria and it's useful for studying and exploiting animals' fecal actinobacteria.

Exploring Actinobacteria assemblages in coastal marine sediments under contrasted Human influences in the West Istria Sea, Croatia.

PubMed

Duran, Robert; Bielen, Ana; Paradžik, Tina; Gassie, Claire; Pustijanac, Emina; Cagnon, Christine; Hamer, Bojan; Vujaklija, Dušica

2015-10-01

The exploration of marine Actinobacteria has as major challenge to answer basic questions of microbial ecology that, in turn, will provide useful information to exploit Actinobacteria metabolisms in biotechnological processes. The ecological functions performed by Actinobacteria in marine sediments are still unclear and belongs to the most burning basic questions. The comparison of Actinobacteria communities inhabiting marine sediments that are under the influence of different contamination types will provide valuable information in the adaptation capacities of Actinobacteria to colonize specific ecological niche. In the present study, the characterization of different Actinobacteria assemblages according to contamination type revealed the ecological importance of Actinobacteria for maintaining both general biogeochemical functions through a "core" Actinobacteria community and specific roles associated with the presence of contaminants. Indeed, the results allowed to distinguish Actinobacteria genera and species operational taxonomic units (OTUs) able to cope with the presence of either (i) As, (ii) metals Ni, Fe, V, Cr, and Mn, or (iii) polycyclic aromatic hydrocarbons (PAHs) and toxic metals (Hg, Cd, Cu, Pb, and Zn). Such observations highlighted the metabolic capacities of Actinobacteria and their potential that should be taken into consideration and advantage during the implementation of bioremediation processes in marine ecosystems.

[Biodiversity and enzymes of culturable facultative-alkaliphilic actinobacteria in saline-alkaline soil in Fukang, Xinjiang].

PubMed

Zhang, Yongguang; Liu, Qing; Wang, Hongfei; Zhang, Daofeng; Chen, Jiyue; Zhang, Yuanming; Li, Wenjun

2014-02-04

In order to analyze the biodiversity of cultivable facultative-alkaliphilic actinobacteria and the enzymes they produced. Total 10 soil samples were collected from saline-alkaline environments of Fukang, Xinjiang province. Facultative-alkaliphilic actinobacteria strains were isolated and identified by 16S rRNA gene sequence analysis. Enzymes including amylase, proteinase, xylanase, and cellulase were detected. Total 116 facultative-alkaliphilic actinobacterial strains and 4 alkali-tolerant actinobacterial strains were isolated from the samples, and those strains were distributed within 22 genera in 13 families and 8 orders of actinobacteria based on their 16S rRNA gene sequence analysis. The ratio of non-predominant Streptomyces and Nocardiopsis strains were 53.3%. The positive rates of amylase, proteinase, xylanase and cellulase were 35.8, 37.6, 28.3 and 17.5%, respectively. Diverse facultative-alkaliphilic actinobacteria were discovered from saline-alkaline environments of Fukang. Facultative-alkaliphilic actinobacteria are a potential source for enzymes. The study would facilitate the knowledge of the diversity of facultative-alkaliphilic actinobacteria, and provide the technical basis for exploration of facultative-alkaliphilic actinobacteria resources.

Isolation of Novel Bacteria Including Rarely Cultivated Phyla, Acidobacteria and Verrucomicrobia, from the Roots of Emergent Plants by Simple Culturing Method

PubMed Central

Tanaka, Yasuhiro; Matsuzawa, Hiroaki; Tamaki, Hideyuki; Tagawa, Masahiro; Toyama, Tadashi; Kamagata, Yoichi; Mori, Kazuhiro

2017-01-01

A number of novel bacteria including members of rarely cultivated phyla, Acidobacteria and Verrucomicrobia, were successfully isolated from the roots of two emergent plants, Iris pseudacorus and Scirpus juncoides, by a simple culturing method. A total of 47.1% (66 strains) for I. pseudacorus and 42.1% (59 strains) for S. juncoides of all isolates (140 strains from each sample) were phylogenetically novel. Furthermore, Acidobacteria and Verrucomicrobia occupied 10.7% (15 strains) and 2.9% (4 strains) of I. pseudacorus isolates, and 2.1% (3 strains) and 3.6% (5 strains) of S. juncoides isolates, respectively, indicating that plant roots are attractive sources for isolating rarely cultivated microbes. PMID:28740039

Quorum Sensing: An Under-Explored Phenomenon in the Phylum Actinobacteria

PubMed Central

Polkade, Ashish V.; Mantri, Shailesh S.; Patwekar, Umera J.; Jangid, Kamlesh

2016-01-01

Quorum sensing is known to play a major role in the regulation of secondary metabolite production, especially, antibiotics, and morphogenesis in the phylum Actinobacteria. Although it is one of the largest bacterial phylum, only 25 of the 342 genera have been reported to use quorum sensing. Of these, only nine have accompanying experimental evidence; the rest are only known through bioinformatic analysis of gene/genome sequences. It is evident that this important communication mechanism is not extensively explored in Actinobacteria. In this review, we summarize the different quorum sensing systems while identifying the limitations of the existing screening strategies and addressing the improvements that have taken place in this field in recent years. The γ-butyrolactone system turned out to be almost exclusively limited to this phylum. In addition, methylenomycin furans, AI-2 and other putative AHL-like signaling molecules are also reported in Actinobacteria. The lack of existing screening systems in detecting minute quantities and of a wider range of signaling molecules was a major reason behind the limited information available on quorum sensing in this phylum. However, recent improvements in screening strategies hold a promising future and are likely to increase the discovery of new signaling molecules. Further, the quorum quenching ability in many Actinobacteria has a great potential in controlling the spread of plant and animal pathogens. A systematic and coordinated effort is required to screen and exploit the enormous potential that quorum sensing in the phylum Actinobacteria has to offer for human benefit. PMID:26904007

In-vitro antimicrobial activity of marine actinobacteria against multidrug resistance Staphylococcus aureus

PubMed Central

Sathish, Kumar SR; Kokati, Venkata Bhaskara Rao

2012-01-01

Objective To investigate the antibacterial activity of marine actinobacteria against multidrug resistance Staphylococcus aureus (MDRSA). Methods Fifty one actinobacterial strains were isolated from salt pans soil, costal area in Kothapattanam, Ongole, Andhra Pradesh. Primary screening was done using cross-streak method against MDRSA. The bioactive compounds are extracted from efficient actinobacteria using solvent extraction. The antimicrobial activity of crude and solvent extracts was performed using Kirby-Bauer method. MIC for ethyl acetate extract was determined by modified agar well diffusion method. The potent actinobacteria are identified using Nonomura key, Shirling and Gottlieb 1966 with Bergey's manual of determinative bacteriology. Results Among the fifty one isolates screened for antibacterial activity, SRB25 were found efficient against MDRSA. The ethyl acetate extracts showed high inhibition against test organism. MIC test was performed with the ethyl acetate extract against MDRSA and found to be 1 000 µg/mL. The isolated actinobacteria are identified as Streptomyces sp with the help of Nonomura key. Conclusions The current investigation reveals that the marine actinobacteria from salt pan environment can be able to produce new drug molecules against drug resistant microorganisms. PMID:23569848

Evidence for Widespread Associations between Neotropical Hymenopteran Insects and Actinobacteria

PubMed Central

Matarrita-Carranza, Bernal; Moreira-Soto, Rolando D.; Murillo-Cruz, Catalina; Mora, Marielos; Currie, Cameron R.; Pinto-Tomas, Adrián A.

2017-01-01

The evolutionary success of hymenopteran insects has been associated with complex physiological and behavioral defense mechanisms against pathogens and parasites. Among these strategies are symbiotic associations between Hymenoptera and antibiotic-producing Actinobacteria, which provide protection to insect hosts. Herein, we examine associations between culturable Actinobacteria and 29 species of tropical hymenopteran insects that span five families, including Apidae (bees), Vespidae (wasps), and Formicidae (ants). In total, 197 Actinobacteria isolates were obtained from 22 of the 29 different insect species sampled. Through 16S rRNA gene sequences of 161 isolates, we show that 91% of the symbionts correspond to members of the genus Streptomyces with less common isolates belonging to Pseudonocardia and Amycolatopsis. Electron microscopy revealed the presence of filamentous bacteria with Streptomyces morphology in brood chambers of two different species of the eusocial wasps. Four fungal strains in the family Ophiocordycipitacea (Hypocreales) known to be specialized insect parasites were also isolated. Bioassay challenges between the Actinobacteria and their possible targeted pathogenic antagonist (both obtained from the same insect at the genus or species level) provide evidence that different Actinobacteria isolates produced antifungal activity, supporting the hypothesis of a defensive association between the insects and these microbe species. Finally, phylogenetic analysis of 16S rRNA and gyrB demonstrate the presence of five Streptomyces lineages associated with a broad range of insect species. Particularly our Clade I is of much interest as it is composed of one 16S rRNA phylotype repeatedly isolated from different insect groups in our sample. This phylotype corresponds to a previously described lineage of host-associated Streptomyces. These results suggest Streptomyces Clade I is a Hymenoptera host-associated lineage spanning several new insect taxa and

Identification of novel potential acetate-oxidizing bacteria in an acetate-fed methanogenic chemostat based on DNA stable isotope probing.

PubMed

Wang, Hui-Zhong; Gou, Min; Yi, Yue; Xia, Zi-Yuan; Tang, Yue-Qin

2018-05-11

Acetate is a significant intermediate of anaerobic fermentation. There are two pathways for converting acetate to CH 4 and CO 2 : acetoclastic methanogenesis by acetoclastic methanogens, and syntrophic acetate oxidation by acetate-oxidizing bacteria (AOB) and hydrogenotrophic methanogens. Detailed investigations of syntrophic acetate-oxidizing bacteria (SAOB) should contribute to the elucidation of the microbial mechanisms of methanogenesis. In this study, we investigated the major phylogenetic groups of acetate-utilizing bacteria (AUB) in a mesophilic methanogenic chemostat fed with acetate as the sole carbon source by using DNA stable isotope probing (SIP) technology. The results indicated that acetoclastic methanogenesis and acetate oxidization/hydrogenotrophic methanogenesis coexisted in the mesophilic chemostat fed with acetate, operated at a dilution rate of 0.1 d -1 . OTU Ace13(9-17) (KU869530), Ace13(9-4) (KU667241), and Ace13(9-23) (KU667236), assigned to the phyla Firmicutes and Bacteroidetes, were probably potential SAOB in the chemostat, which needs further investigation. Species in the phyla Proteobacteria, Deferribacteres, Acidobacteria, Spirochaetes and Actinobacteria were probably capable of utilizing acetate for their growth. Methanoculleus was likely to be the preferred hydrogenotrophic methanogen for syntrophy with AOB in the chemostat.

16S rRNA Gene-Based Metagenomic Analysis of Ozark Cave Bacteria.

PubMed

Oliveira, Cássia; Gunderman, Lauren; Coles, Cathryn A; Lochmann, Jason; Parks, Megan; Ballard, Ethan; Glazko, Galina; Rahmatallah, Yasir; Tackett, Alan J; Thomas, David J

2017-09-01

The microbial diversity within cave ecosystems is largely unknown. Ozark caves maintain a year-round stable temperature (12-14 °C), but most parts of the caves experience complete darkness. The lack of sunlight and geological isolation from surface-energy inputs generate nutrient-poor conditions that may limit species diversity in such environments. Although microorganisms play a crucial role in sustaining life on Earth and impacting human health, little is known about their diversity, ecology, and evolution in community structures. We used five Ozark region caves as test sites for exploring bacterial diversity and monitoring long-term biodiversity. Illumina MiSeq sequencing of five cave soil samples and a control sample revealed a total of 49 bacterial phyla, with seven major phyla: Proteobacteria, Acidobacteria, Actinobacteria, Firmicutes, Chloroflexi, Bacteroidetes, and Nitrospirae. Variation in bacterial composition was observed among the five caves studied. Sandtown Cave had the lowest richness and most divergent community composition. 16S rRNA gene-based metagenomic analysis of cave-dwelling microbial communities in the Ozark caves revealed that species abundance and diversity are vast and included ecologically, agriculturally, and economically relevant taxa.

16S rRNA Gene-Based Metagenomic Analysis of Ozark Cave Bacteria

PubMed Central

Oliveira, Cássia; Gunderman, Lauren; Coles, Cathryn A.; Lochmann, Jason; Parks, Megan; Ballard, Ethan; Glazko, Galina; Rahmatallah, Yasir; Tackett, Alan J.; Thomas, David J.

2018-01-01

The microbial diversity within cave ecosystems is largely unknown. Ozark caves maintain a year-round stable temperature (12–14 °C), but most parts of the caves experience complete darkness. The lack of sunlight and geological isolation from surface-energy inputs generate nutrient-poor conditions that may limit species diversity in such environments. Although microorganisms play a crucial role in sustaining life on Earth and impacting human health, little is known about their diversity, ecology, and evolution in community structures. We used five Ozark region caves as test sites for exploring bacterial diversity and monitoring long-term biodiversity. Illumina MiSeq sequencing of five cave soil samples and a control sample revealed a total of 49 bacterial phyla, with seven major phyla: Proteobacteria, Acidobacteria, Actinobacteria, Firmicutes, Chloroflexi, Bacteroidetes, and Nitrospirae. Variation in bacterial composition was observed among the five caves studied. Sandtown Cave had the lowest richness and most divergent community composition. 16S rRNA gene-based metagenomic analysis of cave-dwelling microbial communities in the Ozark caves revealed that species abundance and diversity are vast and included ecologically, agriculturally, and economically relevant taxa. PMID:29551950

Influence of substrate type on microbial community structure in vertical-flow constructed wetland treating polluted river water.

PubMed

Guan, Wei; Yin, Min; He, Tao; Xie, Shuguang

2015-10-01

Microorganisms attached on the surfaces of substrate materials in constructed wetland play crucial roles in the removal of organic and inorganic pollutants. However, the impact of substrate material on wetland microbial community structure remains unclear. Moreover, little is known about microbial community in constructed wetland purifying polluted surface water. In this study, Illumina high-throughput sequencing was applied to profile the spatial variation of microbial communities in three pilot-scale surface water constructed wetlands with different substrate materials (sand, zeolite, and gravel). Bacterial community diversity and structure showed remarkable spatial variation in both sand and zeolite wetland systems, but changed slightly in gravel wetland system. Bacterial community was found to be significantly influenced by wetland substrate type. A number of bacterial groups were detected in wetland systems, including Proteobacteria, Chloroflexi, Bacteroidetes, Acidobacteria, Cyanobacteria, Nitrospirae, Planctomycetes, Actinobacteria, Firmicutes, Chlorobi, Spirochaetae, Gemmatimonadetes, Deferribacteres, OP8, WS3, TA06, and OP3, while Proteobacteria (accounting for 29.1-62.3 %), mainly composed of Alpha-, Beta-, Gamma-, and Deltaproteobacteria, showed the dominance and might contribute to the effective reduction of organic pollutants. In addition, Nitrospira-like microorganisms were abundant in surface water constructed wetlands.

Exploring the dynamics of bacterial community composition in soil: the pan-bacteriome approach.

PubMed

Bacci, Giovanni; Ceccherini, Maria Teresa; Bani, Alessia; Bazzicalupo, Marco; Castaldini, Maurizio; Galardini, Marco; Giovannetti, Luciana; Mocali, Stefano; Pastorelli, Roberta; Pantani, Ottorino Luca; Arfaioli, Paola; Pietramellara, Giacomo; Viti, Carlo; Nannipieri, Paolo; Mengoni, Alessio

2015-03-01

We performed a longitudinal study (repeated observations of the same sample over time) to investigate both the composition and structure of temporal changes of bacterial community composition in soil mesocosms, subjected to three different treatments (water and 5 or 25 mg kg(-1) of dried soil Cd(2+)). By analogy with the pan genome concept, we identified a core bacteriome and an accessory bacteriome. Resident taxa were assigned to the core bacteriome, while occasional taxa were assigned to the accessory bacteriome. Core and accessory bacteriome represented roughly 35 and 50 % of the taxa detected, respectively, and were characterized by different taxonomic signatures from phylum to genus level while 15 % of the taxa were found to be unique to a particular sample. In particular, the core bacteriome was characterized by higher abundance of members of Planctomycetes, Actinobacteria, Verrucomicrobia and Acidobacteria, while the accessory bacteriome included more members of Firmicutes, Clamydiae and Proteobacteria, suggesting potentially different responses to environmental changes of members from these phyla. We conclude that the pan-bacteriome model may be a useful approach to gain insight for modeling bacterial community structure and inferring different abilities of bacteria taxa.

Identification of the microbial community composition and structure of coal-mine wastewater treatment plants.

PubMed

Ma, Qiao; Qu, Yuan-Yuan; Zhang, Xu-Wang; Shen, Wen-Li; Liu, Zi-Yan; Wang, Jing-Wei; Zhang, Zhao-Jing; Zhou, Ji-Ti

2015-06-01

The wastewater from coal-mine industry varies greatly and is resistant to biodegradation for containing large quantities of inorganic and organic pollutants. Microorganisms in activated sludge are responsible for the pollutants' removal, whereas the microbial community composition and structure are far from understood. In the present study, the sludges from five coal-mine wastewater treatment plants were collected and the microbial communities were analyzed by Illumina high-throughput sequencing. The diversities of these sludges were lower than that of the municipal wastewater treatment systems. The most abundant phylum was Proteobacteria ranging from 63.64% to 96.10%, followed by Bacteroidetes (7.26%), Firmicutes (5.12%), Nitrospira (2.02%), Acidobacteria (1.31%), Actinobacteria (1.30%) and Planctomycetes (0.95%). At genus level, Thiobacillus and Comamonas were the two primary genera in all sludges, other major genera included Azoarcus, Thauera, Pseudomonas, Ohtaekwangia, Nitrosomonas and Nitrospira. Most of these core genera were closely related with aromatic hydrocarbon degradation and denitrification processes. Identification of the microbial communities in coal-mine wastewater treatment plants will be helpful for wastewater management and control. Copyright © 2015 Elsevier GmbH. All rights reserved.

Global and local-scale variation in bacterial community structure of snow from the Swiss and Australian Alps.

PubMed

Wunderlin, Tina; Ferrari, Belinda; Power, Michelle

2016-09-01

Seasonally, snow environments cover up to 50% of the land's surface, yet the microbial diversity and ecosystem functioning within snow, particularly from alpine regions are not well described. This study explores the bacterial diversity in snow using next-generation sequencing technology. Our data expand the global inventory of snow microbiomes by focusing on two understudied regions, the Swiss Alps and the Australian Alps. A total biomass similar to cell numbers in polar snow was detected, with 5.2 to 10.5 × 10(3) cells mL(-1) of snow. We found that microbial community structure of surface snow varied by country and site and along the altitudinal range (alpine and sub-alpine). The bacterial communities present were diverse, spanning 25 distinct phyla, but the six phyla Proteobacteria (Alpha- and Betaproteobacteria), Acidobacteria, Actinobacteria, Bacteroidetes, Cyanobacteria and Firmicutes, accounted for 72%-98% of the total relative abundance. Taxa such as Acidobacteriaceae and Methylocystaceae, associated with cold soils, may be part of the atmospherically sourced snow community, while families like Sphingomonadaceae were detected in every snow sample and are likely part of the common snow biome. © FEMS 2016. All rights reserved. For permissions, please e-mail: journals.permissions@oup.com.

Pilot-Scale Hydrolysis-Aerobic Treatment for Actual Municipal Wastewater: Performance and Microbial Community Analysis

PubMed Central

Bian, Xiao; Wang, Kaijun

2018-01-01

Low-energy cost wastewater treatment is required to change its current energy-intensive status. Although promising, the direct anaerobic digestion of municipal wastewater treatment faces challenges such as low organic content and low temperature, which require further development. The hydrolysis-aerobic system investigated in this study utilized the two well-proven processes of hydrolysis and aerobic oxidation. These have the advantages of efficient COD removal and biodegradability improvement with limited energy cost due to their avoidance of aeration. A pilot-scale hydrolysis-aerobic system was built for performance evaluation with actual municipal wastewater as feed. Results indicated that as high as 39–47% COD removal was achieved with a maximum COD load of 1.10 kg/m3·d. The dominant bacteria phyla included Proteobacteria (36.0%), Planctomycetes (15.4%), Chloroflexi (9.7%), Bacteroidetes (7.7%), Firmicutes (4.4%), Acidobacteria (2.5%), Actinobacteria (1.8%) and Synergistetes (1.3%), while the dominant genera included Thauera (3.42%) and Dechloromonas (3.04%). The absence of methanogens indicates that the microbial community was perfectly retained in the hydrolysis stage instead of in the methane-producing stage. PMID:29522450

Microbial composition in microcosms amended with natural and mineral fertilizers under different water regimes

NASA Astrophysics Data System (ADS)

Brad, Traian; Chiriac, Cecilia; Szekeres, Edina; Coman, Cristian; Rudi, Knut; Sandor, Mignon

2017-04-01

Twenty microcosm enclosures containing two types of soil (i.e. a rich Chernozemic and a poorer soil) were fertilized with mineral (NPK-complex) and organic (Gülle, manure and a green fertilizer) materials and placed under dry and wet water regimes. After 10, 20 and 30 days of the experiment, soil samples were analyzed for the structure and composition of microbial communities using next generation sequencing techniques (Illumina) and statistical analysis. The differences between bacteria communities in different soil types, and in different fertilization and hydric treatments were analyzed using quantitative phylogenetic distances and the ANOSIM test. The two types of soil especially selected for the structure of microbial communities, while moisture and the type of fertilizer appeared to have a smaller influence on microbial diversity in microcosms. The alpha-diversity indices (species richness, evenness and phylogenetic diversity) had higher values for the poorer soil compared to the rich Chernozemic soil. For both soil types, the highest bacteria diversity values were obtained after fertilization with manure. The microbial communities in the analyzed soils were complex and dominated by sequences belonging to Actinobacteria, Proteobacteria, Acidobacteria and Firmicutes.

Genomics of Actinobacteria: Tracing the Evolutionary History of an Ancient Phylum†

PubMed Central

Ventura, Marco; Canchaya, Carlos; Tauch, Andreas; Chandra, Govind; Fitzgerald, Gerald F.; Chater, Keith F.; van Sinderen, Douwe

2007-01-01

Summary: Actinobacteria constitute one of the largest phyla among Bacteria and represent gram-positive bacteria with a high G+C content in their DNA. This bacterial group includes microorganisms exhibiting a wide spectrum of morphologies, from coccoid to fragmenting hyphal forms, as well as possessing highly variable physiological and metabolic properties. Furthermore, Actinobacteria members have adopted different lifestyles, and can be pathogens (e.g., Corynebacterium, Mycobacterium, Nocardia, Tropheryma, and Propionibacterium), soil inhabitants (Streptomyces), plant commensals (Leifsonia), or gastrointestinal commensals (Bifidobacterium). The divergence of Actinobacteria from other bacteria is ancient, making it impossible to identify the phylogenetically closest bacterial group to Actinobacteria. Genome sequence analysis has revolutionized every aspect of bacterial biology by enhancing the understanding of the genetics, physiology, and evolutionary development of bacteria. Various actinobacterial genomes have been sequenced, revealing a wide genomic heterogeneity probably as a reflection of their biodiversity. This review provides an account of the recent explosion of actinobacterial genomics data and an attempt to place this in a biological and evolutionary context. PMID:17804669

Effects of Oxygen on Biodegradation of Fuels in a Corroding Environment

DTIC Science & Technology

2013-06-12

Planctomycetes o Lentisphaerae • Firmicutes • Chloroflexi oChlamydiae • Bacteroidetes • Actinobacteria 100% 90% Q) (,) 80% r:::: ca 70% "C r... Actinobacteria 1.4%~ 2.1 % Chlamydiae 1.4% Lentisphaerae 22.4% 35.0% V errucomicrobia 2.1 % Planctomycetes 6.8% 10.2% 12.5% Bacteroidetes 30.1 % 17.0% 14.0

Littoral lichens as a novel source of potentially bioactive Actinobacteria.

PubMed

Parrot, Delphine; Antony-Babu, Sanjay; Intertaglia, Laurent; Grube, Martin; Tomasi, Sophie; Suzuki, Marcelino T

2015-10-30

Cultivable Actinobacteria are the largest source of microbially derived bioactive molecules. The high demand for novel antibiotics highlights the need for exploring novel sources of these bacteria. Microbial symbioses with sessile macro-organisms, known to contain bioactive compounds likely of bacterial origin, represent an interesting and underexplored source of Actinobacteria. We studied the diversity and potential for bioactive-metabolite production of Actinobacteria associated with two marine lichens (Lichina confinis and L. pygmaea; from intertidal and subtidal zones) and one littoral lichen (Roccella fuciformis; from supratidal zone) from the Brittany coast (France), as well as the terrestrial lichen Collema auriforme (from a riparian zone, Austria). A total of 247 bacterial strains were isolated using two selective media. Isolates were identified and clustered into 101 OTUs (98% identity) including 51 actinobacterial OTUs. The actinobacterial families observed were: Brevibacteriaceae, Cellulomonadaceae, Gordoniaceae, Micrococcaceae, Mycobacteriaceae, Nocardioidaceae, Promicromonosporaceae, Pseudonocardiaceae, Sanguibacteraceae and Streptomycetaceae. Interestingly, the diversity was most influenced by the selective media rather than lichen species or the level of lichen thallus association. The potential for bioactive-metabolite biosynthesis of the isolates was confirmed by screening genes coding for polyketide synthases types I and II. These results show that littoral lichens are a source of diverse potentially bioactive Actinobacteria.

Littoral lichens as a novel source of potentially bioactive Actinobacteria

PubMed Central

Parrot, Delphine; Antony-Babu, Sanjay; Intertaglia, Laurent; Grube, Martin; Tomasi, Sophie; Suzuki, Marcelino T.

2015-01-01

Cultivable Actinobacteria are the largest source of microbially derived bioactive molecules. The high demand for novel antibiotics highlights the need for exploring novel sources of these bacteria. Microbial symbioses with sessile macro-organisms, known to contain bioactive compounds likely of bacterial origin, represent an interesting and underexplored source of Actinobacteria. We studied the diversity and potential for bioactive-metabolite production of Actinobacteria associated with two marine lichens (Lichina confinis and L. pygmaea; from intertidal and subtidal zones) and one littoral lichen (Roccella fuciformis; from supratidal zone) from the Brittany coast (France), as well as the terrestrial lichen Collema auriforme (from a riparian zone, Austria). A total of 247 bacterial strains were isolated using two selective media. Isolates were identified and clustered into 101 OTUs (98% identity) including 51 actinobacterial OTUs. The actinobacterial families observed were: Brevibacteriaceae, Cellulomonadaceae, Gordoniaceae, Micrococcaceae, Mycobacteriaceae, Nocardioidaceae, Promicromonosporaceae, Pseudonocardiaceae, Sanguibacteraceae and Streptomycetaceae. Interestingly, the diversity was most influenced by the selective media rather than lichen species or the level of lichen thallus association. The potential for bioactive-metabolite biosynthesis of the isolates was confirmed by screening genes coding for polyketide synthases types I and II. These results show that littoral lichens are a source of diverse potentially bioactive Actinobacteria. PMID:26514347

Diversity and Seasonal Dynamics of Actinobacteria Populations in Four Lakes in Northeastern Germany

PubMed Central

Allgaier, Martin; Grossart, Hans-Peter

2006-01-01

The phylogenetic diversity and seasonal dynamics of freshwater Actinobacteria populations in four limnologically different lakes of the Mecklenburg-Brandenburg Lake District (northeastern Germany) were investigated. Fluorescence in situ hybridization was used to determine the seasonal abundances and dynamics of total Actinobacteria (probe HGC69a) and the three actinobacterial subclusters acI, acI-A, and acI-B (probes AcI-852, AcI-840-1, and AcI-840-2). Seasonal means of total Actinobacteria abundances in the epilimnia of the lakes varied from 13 to 36%, with maximum values of 30 to 58%, of all DAPI (4′,6′-diamidino-2-phenylindole)-stained cells. Around 80% of total Actinobacteria belonged to the acI cluster. The two subclusters acI-A and acI-B accounted for 60 to 91% of the acI cluster and showed seasonal means of 49% (acI-B) and 23% (acI-A) in relation to the acI cluster. Total Actinobacteria and members of the clusters acI and acI-B showed distinct seasonal changes in their absolute abundances, with maxima in late spring and fall/winter. In eight clone libraries constructed from the lakes, a total of 76 actinobacterial 16S rRNA gene sequences were identified from a total of 177 clones. The majority of the Actinobacteria sequences belonged to the acI and acIV cluster. Several new clusters and subclusters were found (acSTL, scB1-4, and acIVA-D). The majority of all obtained 16S rRNA gene sequences are distinct from those of already-cultured freshwater Actinobacteria. PMID:16672495

Response of Archaeal and Bacterial Soil Communities to Changes Associated with Outdoor Cattle Overwintering.

PubMed

Chroňáková, Alica; Schloter-Hai, Brigitte; Radl, Viviane; Endesfelder, David; Quince, Christopher; Elhottová, Dana; Šimek, Miloslav; Schloter, Michael

2015-01-01

Archaea and bacteria are important drivers for nutrient transformations in soils and catalyse the production and consumption of important greenhouse gases. In this study, we investigate changes in archaeal and bacterial communities of four Czech grassland soils affected by outdoor cattle husbandry. Two show short-term (3 years; STI) and long-term impact (17 years; LTI), one is regenerating from cattle impact (REG) and a control is unaffected by cattle (CON). Cattle manure (CMN), the source of allochthonous microbes, was collected from the same area. We used pyrosequencing of 16S rRNA genes to assess the composition of archaeal and bacterial communities in each soil type and CMN. Both short- and long- term cattle impact negatively altered archaeal and bacterial diversity, leading to increase of homogenization of microbial communities in overwintering soils over time. Moreover, strong shifts in the prokaryotic communities were observed in response to cattle overwintering, with the greatest impact on archaea. Oligotrophic and acidophilic microorganisms (e.g. Thaumarchaeota, Acidobacteria, and α-Proteobacteria) dominated in CON and expressed strong negative response to increased pH, total C and N. Whereas copiotrophic and alkalophilic microbes (e.g. methanogenic Euryarchaeota, Firmicutes, Chloroflexi, Actinobacteria, and Bacteroidetes) were common in LTI showing opposite trends. Crenarchaeota were also found in LTI, though their trophic interactions remain cryptic. Firmicutes, Bacteroidetes, Methanobacteriaceae, and Methanomicrobiaceae indicated the introduction and establishment of faecal microbes into the impacted soils, while Chloroflexi and Methanosarcinaceae suggested increased abundance of soil-borne microbes under altered environmental conditions. The observed changes in prokaryotic community composition may have driven corresponding changes in soil functioning.

Impact of Long-Term Diesel Contamination on Soil Microbial Community Structure

PubMed Central

Maphosa, Farai; Morillo, Jose A.; Abu Al-Soud, Waleed; Langenhoff, Alette A. M.; Grotenhuis, Tim; Rijnaarts, Huub H. M.; Smidt, Hauke

2013-01-01

Microbial community composition and diversity at a diesel-contaminated railway site were investigated by pyrosequencing of bacterial and archaeal 16S rRNA gene fragments to understand the interrelationships among microbial community composition, pollution level, and soil geochemical and physical properties. To this end, 26 soil samples from four matrix types with various geochemical characteristics and contaminant concentrations were investigated. The presence of diesel contamination significantly impacted microbial community composition and diversity, regardless of the soil matrix type. Clean samples showed higher diversity than contaminated samples (P < 0.001). Bacterial phyla with high relative abundances in all samples included Proteobacteria, Firmicutes, Actinobacteria, Acidobacteria, and Chloroflexi. High relative abundances of Archaea, specifically of the phylum Euryarchaeota, were observed in contaminated samples. Redundancy analysis indicated that increased relative abundances of the phyla Chloroflexi, Firmicutes, and Euryarchaeota correlated with the presence of contamination. Shifts in the chemical composition of diesel constituents across the site and the abundance of specific operational taxonomic units (OTUs; defined using a 97% sequence identity threshold) in contaminated samples together suggest that natural attenuation of contamination has occurred. OTUs with sequence similarity to strictly anaerobic Anaerolineae within the Chloroflexi, as well as to Methanosaeta of the phylum Euryarchaeota, were detected. Anaerolineae and Methanosaeta are known to be associated with anaerobic degradation of oil-related compounds; therefore, their presence suggests that natural attenuation has occurred under anoxic conditions. This research underscores the usefulness of next-generation sequencing techniques both to understand the ecological impact of contamination and to identify potential molecular proxies for detection of natural attenuation. PMID:23144139

Plant and Bird Presence Strongly Influences the Microbial Communities in Soils of Admiralty Bay, Maritime Antarctica

PubMed Central

Teixeira, Lia C. R. S.; Yeargeau, Etienne; Balieiro, Fabiano C.; Piccolo, Marisa C.; Peixoto, Raquel S.; Greer, Charles W.; Rosado, Alexandre S.

2013-01-01

Understanding the environmental factors that shape microbial communities is crucial, especially in extreme environments, like Antarctica. Two main forces were reported to influence Antarctic soil microbes: birds and plants. Both birds and plants are currently undergoing relatively large changes in their distribution and abundance due to global warming. However, we need to clearly understand the relationship between plants, birds and soil microorganisms. We therefore collected rhizosphere and bulk soils from six different sampling sites subjected to different levels of bird influence and colonized by Colobanthus quitensis and Deschampsia antarctica in Admiralty Bay, King George Island, Maritime Antarctic. Microarray and qPCR assays targeting 16S rRNA genes of specific taxa were used to assess microbial community structure, composition and abundance and analyzed with a range of soil physico-chemical parameters. The results indicated significant rhizosphere effects in four out of the six sites, including areas with different levels of bird influence. Acidobacteria were significantly more abundant in soils with little bird influence (low nitrogen) and in bulk soil. In contrast, Actinobacteria were significantly more abundant in the rhizosphere of both plant species. At two of the sampling sites under strong bird influence (penguin colonies), Firmicutes were significantly more abundant in D. antarctica rhizosphere but not in C. quitensis rhizosphere. The Firmicutes were also positively and significantly correlated to the nitrogen concentrations in the soil. We conclude that the microbial communities in Antarctic soils are driven both by bird and plants, and that the effect is taxa-specific. PMID:23840411

Bacterial diversity in rhizosphere soil from Antarctic vascular plants of Admiralty Bay, maritime Antarctica.

PubMed

Teixeira, Lia C R S; Peixoto, Raquel S; Cury, Juliano C; Sul, Woo Jun; Pellizari, Vivian H; Tiedje, James; Rosado, Alexandre S

2010-08-01

The Antarctic is a pristine environment that contributes to the maintenance of the global climate equilibrium. The harsh conditions of this habitat are fundamental to selecting those organisms able to survive in such an extreme habitat and able to support the relatively simple ecosystems. The DNA of the microbial community associated with the rhizospheres of Deschampsia antarctica Desv (Poaceae) and Colobanthus quitensis (Kunth) BartI (Caryophyllaceae), the only two native vascular plants that are found in Antarctic ecosystems, was evaluated using a 16S rRNA multiplex 454 pyrosequencing approach. This analysis revealed similar patterns of bacterial diversity between the two plant species from different locations, arguing against the hypothesis that there would be differences between the rhizosphere communities of different plants. Furthermore, the phylum distribution presented a peculiar pattern, with a bacterial community structure different from those reported of many other soils. Firmicutes was the most abundant phylum in almost all the analyzed samples, and there were high levels of anaerobic representatives. Also, some phyla that are dominant in most temperate and tropical soils, such as Acidobacteria, were rarely found in the analyzed samples. Analyzing all the sample libraries together, the predominant genera found were Bifidobacterium (phylum Actinobacteria), Arcobacter (phylum Proteobacteria) and Faecalibacterium (phylum Firmicutes). To the best of our knowledge, this is the first major bacterial sequencing effort of this kind of soil, and it revealed more than expected diversity within these rhizospheres of both maritime Antarctica vascular plants in Admiralty Bay, King George Island, which is part of the South Shetlands archipelago.

Plant and bird presence strongly influences the microbial communities in soils of Admiralty Bay, Maritime Antarctica.

PubMed

Teixeira, Lia C R S; Yeargeau, Etienne; Balieiro, Fabiano C; Piccolo, Marisa C; Peixoto, Raquel S; Greer, Charles W; Rosado, Alexandre S

2013-01-01

Understanding the environmental factors that shape microbial communities is crucial, especially in extreme environments, like Antarctica. Two main forces were reported to influence Antarctic soil microbes: birds and plants. Both birds and plants are currently undergoing relatively large changes in their distribution and abundance due to global warming. However, we need to clearly understand the relationship between plants, birds and soil microorganisms. We therefore collected rhizosphere and bulk soils from six different sampling sites subjected to different levels of bird influence and colonized by Colobanthus quitensis and Deschampsia antarctica in Admiralty Bay, King George Island, Maritime Antarctic. Microarray and qPCR assays targeting 16S rRNA genes of specific taxa were used to assess microbial community structure, composition and abundance and analyzed with a range of soil physico-chemical parameters. The results indicated significant rhizosphere effects in four out of the six sites, including areas with different levels of bird influence. Acidobacteria were significantly more abundant in soils with little bird influence (low nitrogen) and in bulk soil. In contrast, Actinobacteria were significantly more abundant in the rhizosphere of both plant species. At two of the sampling sites under strong bird influence (penguin colonies), Firmicutes were significantly more abundant in D. antarctica rhizosphere but not in C. quitensis rhizosphere. The Firmicutes were also positively and significantly correlated to the nitrogen concentrations in the soil. We conclude that the microbial communities in Antarctic soils are driven both by bird and plants, and that the effect is taxa-specific.

Variations in the structure of airborne bacterial communities in Tsogt-Ovoo of Gobi desert area during dust events.

PubMed

Maki, Teruya; Kurosaki, Yasunori; Onishi, Kazunari; Lee, Kevin C; Pointing, Stephen B; Jugder, Dulam; Yamanaka, Norikazu; Hasegawa, Hiroshi; Shinoda, Masato

2017-01-01

Asian dust events transport the airborne bacteria in Chinese desert regions as well as mineral particles and influence downwind area varying biological ecosystems and climate changes. However, the airborne bacterial dynamics were rarely investigated in the Gobi desert area, where dust events are highly frequent. In this study, air samplings were sequentially performed at a 2-m high above the ground at the sampling site located in desert area (Tsogt-Ovoo of Gobi desert; Mongolia 44.2304°N, 105.1700°E). During the dust event days, the bacterial cells and mineral particles increased to more than tenfold of concentrations. MiSeq sequencing targeting 16S ribosomal DNA revealed that the airborne bacteria in desert area mainly belonged to the classes Acidobacteria , Actinobacteria , Bacteroidetes , Chloroflexi , Bacilli , Alpha-proteobacteria , Beta-proteobacteria , and Gamma-proteobacteria. The bacterial community structures were different between dust events and non-dust events. The air samples collected at the dust events indicated high abundance rates of Alpha-proteobacteria , which were reported to dominate on the leaf surfaces of plants or in the saline lake environments. After the dust events, the members of Firmicutes ( Bacilli ) and Bacteroidetes , which are known to form endospore and attach with coarse particles, respectively, increased their relative abundances in the air samples. Presumably, the bacterial compositions and diversities in atmosphere significantly vary during dust events, which carry some particles from grassland (phyllo-sphere), dry lake, and sand surfaces, as well as some bacterial populations such as Firmicutes and Bacteroidetes maintain in the atmosphere for longer time.

Use of denaturing gradient gel electrophoresis to detect Actinobacteria associated with the human faecal microbiota.

PubMed

Hoyles, Lesley; Clear, Jessica A; McCartney, Anne L

2013-08-01

With the exceptions of the bifidobacteria, propionibacteria and coriobacteria, the Actinobacteria associated with the human gastrointestinal tract have received little attention. This has been due to the seeming absence of these bacteria from most clone libraries. In addition, many of these bacteria have fastidious growth and atmospheric requirements. A recent cultivation-based study has shown that the Actinobacteria of the human gut may be more diverse than previously thought. The aim of this study was to develop a denaturing gradient gel electrophoresis (DGGE) approach for characterizing Actinobacteria present in faecal samples. Amount of DNA added to the Actinobacteria-specific PCR used to generate strong PCR products of equal intensity from faecal samples of five infants, nine adults and eight elderly adults was anti-correlated with counts of bacteria obtained using fluorescence in situ hybridization probe HGC69A. A nested PCR using Actinobacteria-specific and universal PCR-DGGE primers was used to generate profiles for the Actinobacteria. Cloning of sequences from the DGGE bands confirmed the specificity of the Actinobacteria-specific primers. In addition to members of the genus Bifidobacterium, species belonging to the genera Propionibacterium, Microbacterium, Brevibacterium, Actinomyces and Corynebacterium were found to be part of the faecal microbiota of healthy humans. Copyright © 2013 Elsevier Ltd. All rights reserved.

Multi-analytical approach reveals potential microbial indicators in soil for sugarcane model systems

DOE Office of Scientific and Technical Information (OSTI.GOV)

Navarrete, Acacio Aparecido; Diniz, Tatiana Rosa; Braga, Lucas Palma Perez

This study focused on the effects of organic and inorganic amendments and straw retention on the microbial biomass (MB) and taxonomic groups of bacteria in sugarcane-cultivated soils in a greenhouse mesocosm experiment monitored for gas emissions and chemical factors. The experiment consisted of combinations of synthetic nitrogen (N), vinasse (V; a liquid waste from ethanol production), and sugarcane-straw blankets. Increases in CO 2-C and N 2O-N emissions were identified shortly after the addition of both N and V to the soils, thus increasing MB nitrogen (MB-N) and decreasing MB carbon (MB-C) in the N+V-amended soils and altering soil chemical factorsmore » that were correlated with the MB. Across 57 soil metagenomic datasets, Actinobacteria (31.5%), Planctomycetes (12.3%), Deltaproteobacteria (12.3%), Alphaproteobacteria (12.0%) and Betaproteobacteria (11.1%) were the most dominant bacterial groups during the experiment. Differences in relative abundance of metagenomic sequences were mainly revealed for Acidobacteria, Actinobacteria, Gammaproteobacteria and Verrucomicrobia with regard to N+V fertilization and straw retention. Differential abundances in bacterial groups were confirmed using 16S rRNA gene-targeted phylum-specific primers for real-time PCR analysis in all soil samples, whose results were in accordance with sequence data, except for Gammaproteobacteria. Actinobacteria were more responsive to straw retention with Rubrobacterales, Bifidobacteriales and Actinomycetales related to the chemical factors of N+V-amended soils. Acidobacteria subgroup 7 and Opitutae, a verrucomicrobial class, were related to the chemical factors of soils without straw retention as a surface blanket. Taken together, the results showed that MB-C and MB-N responded to changes in soil chemical factors and CO 2-C and N 2O-N emissions, especially for N+V-amended soils. The results also indicated that several taxonomic groups of bacteria, such as Acidobacteria, Actinobacteria and

Multi-Analytical Approach Reveals Potential Microbial Indicators in Soil for Sugarcane Model Systems

PubMed Central

Navarrete, Acacio Aparecido; Diniz, Tatiana Rosa; Braga, Lucas Palma Perez; Silva, Genivaldo Gueiros Zacarias; Franchini, Julio Cezar; Rossetto, Raffaella; Edwards, Robert Alan; Tsai, Siu Mui

2015-01-01

This study focused on the effects of organic and inorganic amendments and straw retention on the microbial biomass (MB) and taxonomic groups of bacteria in sugarcane-cultivated soils in a greenhouse mesocosm experiment monitored for gas emissions and chemical factors. The experiment consisted of combinations of synthetic nitrogen (N), vinasse (V; a liquid waste from ethanol production), and sugarcane-straw blankets. Increases in CO2-C and N2O-N emissions were identified shortly after the addition of both N and V to the soils, thus increasing MB nitrogen (MB-N) and decreasing MB carbon (MB-C) in the N+V-amended soils and altering soil chemical factors that were correlated with the MB. Across 57 soil metagenomic datasets, Actinobacteria (31.5%), Planctomycetes (12.3%), Deltaproteobacteria (12.3%), Alphaproteobacteria (12.0%) and Betaproteobacteria (11.1%) were the most dominant bacterial groups during the experiment. Differences in relative abundance of metagenomic sequences were mainly revealed for Acidobacteria, Actinobacteria, Gammaproteobacteria and Verrucomicrobia with regard to N+V fertilization and straw retention. Differential abundances in bacterial groups were confirmed using 16S rRNA gene-targeted phylum-specific primers for real-time PCR analysis in all soil samples, whose results were in accordance with sequence data, except for Gammaproteobacteria. Actinobacteria were more responsive to straw retention with Rubrobacterales, Bifidobacteriales and Actinomycetales related to the chemical factors of N+V-amended soils. Acidobacteria subgroup 7 and Opitutae, a verrucomicrobial class, were related to the chemical factors of soils without straw retention as a surface blanket. Taken together, the results showed that MB-C and MB-N responded to changes in soil chemical factors and CO2-C and N2O-N emissions, especially for N+V-amended soils. The results also indicated that several taxonomic groups of bacteria, such as Acidobacteria, Actinobacteria and

Multi-analytical approach reveals potential microbial indicators in soil for sugarcane model systems

DOE PAGES

Navarrete, Acacio Aparecido; Diniz, Tatiana Rosa; Braga, Lucas Palma Perez; ...

2015-06-09

This study focused on the effects of organic and inorganic amendments and straw retention on the microbial biomass (MB) and taxonomic groups of bacteria in sugarcane-cultivated soils in a greenhouse mesocosm experiment monitored for gas emissions and chemical factors. The experiment consisted of combinations of synthetic nitrogen (N), vinasse (V; a liquid waste from ethanol production), and sugarcane-straw blankets. Increases in CO 2-C and N 2O-N emissions were identified shortly after the addition of both N and V to the soils, thus increasing MB nitrogen (MB-N) and decreasing MB carbon (MB-C) in the N+V-amended soils and altering soil chemical factorsmore » that were correlated with the MB. Across 57 soil metagenomic datasets, Actinobacteria (31.5%), Planctomycetes (12.3%), Deltaproteobacteria (12.3%), Alphaproteobacteria (12.0%) and Betaproteobacteria (11.1%) were the most dominant bacterial groups during the experiment. Differences in relative abundance of metagenomic sequences were mainly revealed for Acidobacteria, Actinobacteria, Gammaproteobacteria and Verrucomicrobia with regard to N+V fertilization and straw retention. Differential abundances in bacterial groups were confirmed using 16S rRNA gene-targeted phylum-specific primers for real-time PCR analysis in all soil samples, whose results were in accordance with sequence data, except for Gammaproteobacteria. Actinobacteria were more responsive to straw retention with Rubrobacterales, Bifidobacteriales and Actinomycetales related to the chemical factors of N+V-amended soils. Acidobacteria subgroup 7 and Opitutae, a verrucomicrobial class, were related to the chemical factors of soils without straw retention as a surface blanket. Taken together, the results showed that MB-C and MB-N responded to changes in soil chemical factors and CO 2-C and N 2O-N emissions, especially for N+V-amended soils. The results also indicated that several taxonomic groups of bacteria, such as Acidobacteria, Actinobacteria and

Anti-Candida Properties of Urauchimycins from Actinobacteria Associated with Trachymyrmex Ants

PubMed Central

Mendes, Thais D.; Borges, Warley S.; Solomon, Scott E.; Vieira, Paulo C.; Duarte, Marta C. T.; Pagnocca, Fernando C.

2013-01-01

After decades of intensive searching for antimicrobial compounds derived from actinobacteria, the frequency of isolation of new molecules has decreased. To cope with this concern, studies have focused on the exploitation of actinobacteria from unexplored environments and actinobacteria symbionts of plants and animals. In this study, twenty-four actinobacteria strains isolated from workers of Trachymyrmex ants were evaluated for antifungal activity towards a variety of Candida species. Results revealed that seven strains inhibited the tested Candida species. Streptomyces sp. TD025 presented potent and broad spectrum of inhibition of Candida and was selected for the isolation of bioactive molecules. From liquid shake culture of this bacterium, we isolated the rare antimycin urauchimycins A and B. For the first time, these molecules were evaluated for antifungal activity against medically important Candida species. Both antimycins showed antifungal activity, especially urauchimycin B. This compound inhibited the growth of all Candida species tested, with minimum inhibitory concentration values equivalent to the antifungal nystatin. Our results concur with the predictions that the attine ant-microbe symbiosis may be a source of bioactive metabolites for biotechnology and medical applications. PMID:23586060

Marine Rare Actinobacteria: Isolation, Characterization, and Strategies for Harnessing Bioactive Compounds

PubMed Central

Dhakal, Dipesh; Pokhrel, Anaya Raj; Shrestha, Biplav; Sohng, Jae Kyung

2017-01-01

Actinobacteria are prolific producers of thousands of biologically active natural compounds with diverse activities. More than half of these bioactive compounds have been isolated from members belonging to actinobacteria. Recently, rare actinobacteria existing at different environmental settings such as high altitudes, volcanic areas, and marine environment have attracted attention. It has been speculated that physiological or biochemical pressures under such harsh environmental conditions can lead to the production of diversified natural compounds. Hence, marine environment has been focused for the discovery of novel natural products with biological potency. Many novel and promising bioactive compounds with versatile medicinal, industrial, or agricultural uses have been isolated and characterized. The natural compounds cannot be directly used as drug or other purposes, so they are structurally modified and diversified to ameliorate their biological or chemical properties. Versatile synthetic biological tools, metabolic engineering techniques, and chemical synthesis platform can be used to assist such structural modification. This review summarizes the latest studies on marine rare actinobacteria and their natural products with focus on recent approaches for structural and functional diversification of such microbial chemicals for attaining better applications. PMID:28663748

High diversity and suggested endemicity of culturable Actinobacteria in an extremely oligotrophic desert oasis

PubMed Central

Arocha-Garza, Hector Fernando; Canales-Del Castillo, Ricardo; Eguiarte, Luis E.; Souza, Valeria

2017-01-01

The phylum Actinobacteria constitutes one of the largest and anciently divergent phyla within the Bacteria domain. Actinobacterial diversity has been thoroughly researched in various environments due to its unique biotechnological potential. Such studies have focused mostly on soil communities, but more recently marine and extreme environments have also been explored, finding rare taxa and demonstrating dispersal limitation and biogeographic patterns for Streptomyces. To test the distribution of Actinobacteria populations on a small scale, we chose the extremely oligotrophic and biodiverse Cuatro Cienegas Basin (CCB), an endangered oasis in the Chihuahuan desert to assess the diversity and uniqueness of Actinobacteria in the Churince System with a culture-dependent approach over a period of three years, using nine selective media. The 16S rDNA of putative Actinobacteria were sequenced using both bacteria universal and phylum-specific primer pairs. Phylogenetic reconstructions were performed to analyze OTUs clustering and taxonomic identification of the isolates in an evolutionary context, using validated type species of Streptomyces from previously phylogenies as a reference. Rarefaction analysis for total Actinobacteria and for Streptomyces isolates were performed to estimate species’ richness in the intermediate lagoon (IL) in the oligotrophic Churince system. A total of 350 morphologically and nutritionally diverse isolates were successfully cultured and characterized as members of the Phylum Actinobacteria. A total of 105 from the total isolates were successfully subcultured, processed for DNA extraction and 16S-rDNA sequenced. All strains belong to the order Actinomycetales, encompassing 11 genera of Actinobacteria; the genus Streptomyces was found to be the most abundant taxa in all the media tested throughout the 3-year sampling period. Phylogenetic analysis of our isolates and another 667 reference strains of the family Streptomycetaceae shows that our

Actinobacteria mediated synthesis of nanoparticles and their biological properties: A review.

PubMed

Manivasagan, Panchanathan; Venkatesan, Jayachandran; Sivakumar, Kannan; Kim, Se-Kwon

2016-01-01

Nanotechnology is gaining tremendous attention in the present century due to its expected impact on many important areas such as medicine, energy, electronics, and space industries. In this context, actinobacterial biosynthesis of nanoparticles is a reliable, eco-friendly, and important aspect of green chemistry approach that interconnects microbial biotechnology and nanobiotechnology. Antibiotics produced by actinobacteria are popular in almost all the therapeutic measures and it is known that these microbes are also helpful in the biosynthesis of nanoparticles with good surface and size characteristics. In fact, actinobacteria are efficient producers of nanoparticles that show a range of biological properties, namely, antibacterial, antifungal, anticancer, anti-biofouling, anti-malarial, anti-parasitic, antioxidant, etc. This review describes the potential use of the actinobacteria as the novel sources for the biosynthesis of nanoparticles with improved biomedical applications.

Real-time image processing for label-free enrichment of Actinobacteria cultivated in picolitre droplets.

PubMed

Zang, Emerson; Brandes, Susanne; Tovar, Miguel; Martin, Karin; Mech, Franziska; Horbert, Peter; Henkel, Thomas; Figge, Marc Thilo; Roth, Martin

2013-09-21

The majority of today's antimicrobial therapeutics is derived from secondary metabolites produced by Actinobacteria. While it is generally assumed that less than 1% of Actinobacteria species from soil habitats have been cultivated so far, classic screening approaches fail to supply new substances, often due to limited throughput and frequent rediscovery of already known strains. To overcome these restrictions, we implement high-throughput cultivation of soil-derived Actinobacteria in microfluidic pL-droplets by generating more than 600,000 pure cultures per hour from a spore suspension that can subsequently be incubated for days to weeks. Moreover, we introduce triggered imaging with real-time image-based droplet classification as a novel universal method for pL-droplet sorting. Growth-dependent droplet sorting at frequencies above 100 Hz is performed for label-free enrichment and extraction of microcultures. The combination of both cultivation of Actinobacteria in pL-droplets and real-time detection of growing Actinobacteria has great potential in screening for yet unknown species as well as their undiscovered natural products.

The obligate respiratory supercomplex from Actinobacteria.

PubMed

Kao, Wei-Chun; Kleinschroth, Thomas; Nitschke, Wolfgang; Baymann, Frauke; Neehaul, Yashvin; Hellwig, Petra; Richers, Sebastian; Vonck, Janet; Bott, Michael; Hunte, Carola

2016-10-01

Actinobacteria are closely linked to human life as industrial producers of bioactive molecules and as human pathogens. Respiratory cytochrome bcc complex and cytochrome aa3 oxidase are key components of their aerobic energy metabolism. They form a supercomplex in the actinobacterial species Corynebacterium glutamicum. With comprehensive bioinformatics and phylogenetic analysis we show that genes for cyt bcc-aa3 supercomplex are characteristic for Actinobacteria (Actinobacteria and Acidimicrobiia, except the anaerobic orders Actinomycetales and Bifidobacteriales). An obligatory supercomplex is likely, due to the lack of genes encoding alternative electron transfer partners such as mono-heme cyt c. Instead, subunit QcrC of bcc complex, here classified as short di-heme cyt c, will provide the exclusive electron transfer link between the complexes as in C. glutamicum. Purified to high homogeneity, the C. glutamicum bcc-aa3 supercomplex contained all subunits and cofactors as analyzed by SDS-PAGE, BN-PAGE, absorption and EPR spectroscopy. Highly uniform supercomplex particles in electron microscopy analysis support a distinct structural composition. The supercomplex possesses a dimeric stoichiometry with a ratio of a-type, b-type and c-type hemes close to 1:1:1. Redox titrations revealed a low potential bcc complex (Em(ISP)=+160mV, Em(bL)=-291mV, Em(bH)=-163mV, Em(cc)=+100mV) fined-tuned for oxidation of menaquinol and a mixed potential aa3 oxidase (Em(CuA)=+150mV, Em(a/a3)=+143/+317mV) mediating between low and high redox potential to accomplish dioxygen reduction. The generated molecular model supports a stable assembled supercomplex with defined architecture which permits energetically efficient coupling of menaquinol oxidation and dioxygen reduction in one supramolecular entity. Copyright © 2016 Elsevier B.V. All rights reserved.

Potential biocontrol actinobacteria: Rhizospheric isolates from the Argentine Pampas lowlands legumes.

PubMed

Solans, Mariana; Scervino, Jose Martin; Messuti, María Inés; Vobis, Gernot; Wall, Luis Gabriel

2016-11-01

Control of fungal plant diseases by using naturally occurring non-pathogenic microorganisms represents a promising approach to biocontrol agents. This study reports the isolation, characterization, and fungal antagonistic activity of actinobacteria from forage soils in the Flooding Pampa, Argentina. A total of 32 saprophytic strains of actinobacteria were obtained by different isolation methods from rhizospheric soil of Lotus tenuis growing in the Salado River Basin. Based on physiological traits, eight isolates were selected for their biocontrol-related activities such as production of lytic extracellular enzymes, siderophores, hydrogen cyanide (HCN), and antagonistic activity against Cercospora sojina, Macrophomia phaseolina, Phomopsis sp., Fusarium oxysporum, and Fusarium verticilloides. These actinobacteria strains were characterized morphologically, physiologically, and identified by using molecular techniques. The characterization of biocontrol-related activities in vitro showed positive results for exoprotease, phospholipase, fungal growth inhibition, and siderophore production. However, none of the strains was positive for the production of hydrogen cyanide (HCN). Streptomyces sp. MM140 presented the highest index for biocontrol, and appear to be promising pathogenic fungi biocontrol agents. These results show the potential capacity of actinobacteria isolated from forage soils in the Argentine Pampas lowlands as promising biocontrol agents, and their future agronomic applications. © 2016 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

Key roles for freshwater Actinobacteria revealed by deep metagenomic sequencing.

PubMed

Ghai, Rohit; Mizuno, Carolina Megumi; Picazo, Antonio; Camacho, Antonio; Rodriguez-Valera, Francisco

2014-12-01

Freshwater ecosystems are critical but fragile environments directly affecting society and its welfare. However, our understanding of genuinely freshwater microbial communities, constrained by our capacity to manipulate its prokaryotic participants in axenic cultures, remains very rudimentary. Even the most abundant components, freshwater Actinobacteria, remain largely unknown. Here, applying deep metagenomic sequencing to the microbial community of a freshwater reservoir, we were able to circumvent this traditional bottleneck and reconstruct de novo seven distinct streamlined actinobacterial genomes. These genomes represent three new groups of photoheterotrophic, planktonic Actinobacteria. We describe for the first time genomes of two novel clades, acMicro (Micrococcineae, related to Luna2,) and acAMD (Actinomycetales, related to acTH1). Besides, an aggregate of contigs belonged to a new branch of the Acidimicrobiales. All are estimated to have small genomes (approximately 1.2 Mb), and their GC content varied from 40 to 61%. One of the Micrococcineae genomes encodes a proteorhodopsin, a rhodopsin type reported for the first time in Actinobacteria. The remarkable potential capacity of some of these genomes to transform recalcitrant plant detrital material, particularly lignin-derived compounds, suggests close linkages between the terrestrial and aquatic realms. Moreover, abundances of Actinobacteria correlate inversely to those of Cyanobacteria that are responsible for prolonged and frequently irretrievable damage to freshwater ecosystems. This suggests that they might serve as sentinels of impending ecological catastrophes. © 2014 John Wiley & Sons Ltd.

Rhizospheric Bacterial Community of Endemic Rhododendron arboreum Sm. Ssp. delavayi along Eastern Himalayan Slope in Tawang

PubMed Central

Debnath, Rajal; Yadav, Archana; Gupta, Vijai K.; Singh, Bhim P.; Handique, Pratap J.; Saikia, Ratul

2016-01-01

Information on rhizosphere microbiome of endemic plants from high mountain ecosystems against those of cultivated plantations is inadequate. Comparative bacterial profiles of endemic medicinal plant Rhododendron arboreum Sm. subsp. delavayi rhizosphere pertaining to four altitudinal zonation Pankang Thang (PTSO), Nagula, Y-junction and Bum La (Indo-China border; in triplicates each) along cold adapted Eastern slope of Himalayan Tawang region, India is described here. Significant differences in DGGE profile between below ground bulk vs. rhizospheric community profile associated with the plant was identified. Tagged 16S amplicon sequencing from PTSO (3912 m) to Bum La (4509 m), revealed that soil pH, total nitrogen (TN), organic matter (OM) significantly influenced the underlying bacterial community structure at different altitudes. The relative abundance of Acidobacteria was inversely related to pH, as opposed to TN which was positively correlated to Acidobacteria and Proteobacteria abundance. TN was also the significant predictor for less abundant taxonomic groups Chloroflexi, Gemmatimonadetes, and Nitrospirae. Bum La soil harbored less bacterial diversity compared to other sites at lower altitudes. The most abundant phyla at 3% genetic difference were Acidobacteria, Actinobacteria, and Proteobacteria amongst others. Analysis of similarity indicated greater similarity within lower altitudinal than higher altitudinal group (ANOSIM, R = 0.287, p = 0.02). Constraining the ordination with the edaphic factor explained 83.13% of variation. Unique phylotypes of Bradyrhizobium and uncultured Rhizobiales were found in significant proportions at the four regions. With over 1% relative abundance Actinobacteria (42.6%), Acidobacteria (24.02%), Proteobacteria (16.00%), AD3 (9.23%), WPS-2 (5.1%), and Chloroflexi (1.48%) dominated the core microbiome. PMID:27642287

Paratrechina longicornis ants in a tropical dry forest harbor specific Actinobacteria diversity.

PubMed

Reyes, Ruth D Hernández; Cafaro, Matías J

2015-01-01

The diversity of Actinobacteria associated with Paratrechina longicornis, an ant species that prefers a high protein diet, in a subtropical dry forest (Guánica, Puerto Rico) was determined by culture methods and by 16S rDNA clone libraries. The results of both methodologies were integrated to obtain a broader view of the diversity. Streptomyces, Actinomadura, Nocardia, Ornithinimicrobium, Tsukamurella, Brevibacterium, Saccharopolyspora, Nocardioides, Microbacterium, Leifsonia, Pseudonocardia, Corynebacterium, Geodermatophilus, Amycolatopsis, and Nonomuraea were found associated with the ants. The genera Streptomyces and Actinomadura were the most abundant. Also, the diversity of Actinobacteria associated with the soil surrounding the nest was determined using 16S rDNA clone libraries. In total, 27 genera of Actinobacteria were associated with the nest soils. A dominant genus was not observed in any of the soil samples. We compared statistically the Actinobacteria communities among P. longicornis nests and each nest with its surrounding soil using the clone libraries data. We established that the communities associated with the ants were consistent and significantly different from those found in the soil in which the ants live. © 2015 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

Endophytic Actinobacteria Associated with Dracaena cochinchinensis Lour.: Isolation, Diversity, and Their Cytotoxic Activities.

PubMed

Salam, Nimaichand; Khieu, Thi-Nhan; Liu, Min-Jiao; Vu, Thu-Trang; Chu-Ky, Son; Quach, Ngoc-Tung; Phi, Quyet-Tien; Narsing Rao, Manik Prabhu; Fontana, Angélique; Sarter, Samira; Li, Wen-Jun

2017-01-01

Dracaena cochinchinensis Lour. is an ethnomedicinally important plant used in traditional Chinese medicine known as dragon's blood. Excessive utilization of the plant for extraction of dragon's blood had resulted in the destruction of the important niche. During a study to provide a sustainable way of utilizing the resources, the endophytic Actinobacteria associated with the plant were explored for potential utilization of their medicinal properties. Three hundred and four endophytic Actinobacteria belonging to the genera Streptomyces , Nocardiopsis , Brevibacterium , Microbacterium , Tsukamurella , Arthrobacter , Brachybacterium , Nocardia , Rhodococcus , Kocuria , Nocardioides , and Pseudonocardia were isolated from different tissues of D. cochinchinensis Lour. Of these, 17 strains having antimicrobial and anthracyclines-producing activities were further selected for screening of antifungal and cytotoxic activities against two human cancer cell lines, MCF-7 and Hep G2. Ten of these selected endophytic Actinobacteria showed antifungal activities against at least one of the fungal pathogens, of which three strains exhibited cytotoxic activities with IC 50 -values ranging between 3 and 33  μ g·mL -1 . Frequencies for the presence of biosynthetic genes, polyketide synthase- (PKS-) I, PKS-II, and nonribosomal peptide synthetase (NRPS) among these 17 selected bioactive Actinobacteria were 29.4%, 70.6%, and 23.5%, respectively. The results indicated that the medicinal plant D. cochinchinensis Lour. is a good niche of biologically important metabolites-producing Actinobacteria.

Endophytic Actinobacteria Associated with Dracaena cochinchinensis Lour.: Isolation, Diversity, and Their Cytotoxic Activities

PubMed Central

Salam, Nimaichand; Khieu, Thi-Nhan; Liu, Min-Jiao; Vu, Thu-Trang; Quach, Ngoc-Tung; Phi, Quyet-Tien; Fontana, Angélique; Sarter, Samira

2017-01-01

Dracaena cochinchinensis Lour. is an ethnomedicinally important plant used in traditional Chinese medicine known as dragon's blood. Excessive utilization of the plant for extraction of dragon's blood had resulted in the destruction of the important niche. During a study to provide a sustainable way of utilizing the resources, the endophytic Actinobacteria associated with the plant were explored for potential utilization of their medicinal properties. Three hundred and four endophytic Actinobacteria belonging to the genera Streptomyces, Nocardiopsis, Brevibacterium, Microbacterium, Tsukamurella, Arthrobacter, Brachybacterium, Nocardia, Rhodococcus, Kocuria, Nocardioides, and Pseudonocardia were isolated from different tissues of D. cochinchinensis Lour. Of these, 17 strains having antimicrobial and anthracyclines-producing activities were further selected for screening of antifungal and cytotoxic activities against two human cancer cell lines, MCF-7 and Hep G2. Ten of these selected endophytic Actinobacteria showed antifungal activities against at least one of the fungal pathogens, of which three strains exhibited cytotoxic activities with IC50-values ranging between 3 and 33 μg·mL−1. Frequencies for the presence of biosynthetic genes, polyketide synthase- (PKS-) I, PKS-II, and nonribosomal peptide synthetase (NRPS) among these 17 selected bioactive Actinobacteria were 29.4%, 70.6%, and 23.5%, respectively. The results indicated that the medicinal plant D. cochinchinensis Lour. is a good niche of biologically important metabolites-producing Actinobacteria. PMID:28484706

Screening of novel actinobacteria and characterization of the potential isolates from mangrove sediment of south coastal India.

PubMed

Arumugam, T; Senthil Kumar, P; Kameshwar, R; Prapanchana, K

2017-06-01

The importance of the current research is to investigate the different types of samples from the various mangrove sediments; as source of actinobacteria from the mangrove wet soil. Potential isolate screening by antimicrobial activity and identified actinobacteria was characterized based on cultural morphology, physiological and biochemical characteristics. Three different types of media were used to isolate actinobacteria from various geographical region of mangrove soil sediment and the genotype locus was recognized by 16S rDNA. Totally 144 actinobacteria isolates were recovered from 10 samples using three media. The most active culture media in the isolation of actinobacteria were ISP2 and Glycerol Yeast Extract Agar. Among 144 isolates, 38 isolates (26.38%) exhibited antimicrobial activity. Out of 38 isolates, potentially active 2 cultures were further supported for morphological and biochemical characterization analysis. Most of the isolates were produced pharmaceutically important enzymes such as protease, amylase, lipase, cellulose and also revealed antimicrobial activity against tested microorganism. The enriched salt, pH and temperature tolerance of the actinobacteria isolates to discharge commercially valuable primary and secondary bioactive metabolites. The present results functionally characterize novel mangrove actinobacteria and their metabolites for commercial interest in pharmaceutical industry. Copyright © 2017 Elsevier Ltd. All rights reserved.

Pyrosequencing-Derived Bacterial, Archaeal, and Fungal Diversity of Spacecraft Hardware Destined for Mars

PubMed Central

Vaishampayan, Parag; Nilsson, Henrik R.; Torok, Tamas; Venkateswaran, Kasthuri

2012-01-01

Spacecraft hardware and assembly cleanroom surfaces (233 m2 in total) were sampled, total genomic DNA was extracted, hypervariable regions of the 16S rRNA gene (bacteria and archaea) and ribosomal internal transcribed spacer (ITS) region (fungi) were subjected to 454 tag-encoded pyrosequencing PCR amplification, and 203,852 resulting high-quality sequences were analyzed. Bioinformatic analyses revealed correlations between operational taxonomic unit (OTU) abundance and certain sample characteristics, such as source (cleanroom floor, ground support equipment [GSE], or spacecraft hardware), cleaning regimen applied, and location about the facility or spacecraft. National Aeronautics and Space Administration (NASA) cleanroom floor and GSE surfaces gave rise to a larger number of diverse bacterial communities (619 OTU; 20 m2) than colocated spacecraft hardware (187 OTU; 162 m2). In contrast to the results of bacterial pyrosequencing, where at least some sequences were generated from each of the 31 sample sets examined, only 13 and 18 of these sample sets gave rise to archaeal and fungal sequences, respectively. As was the case for bacteria, the abundance of fungal OTU in the GSE surface samples dramatically diminished (9× less) once cleaning protocols had been applied. The presence of OTU representative of actinobacteria, deinococci, acidobacteria, firmicutes, and proteobacteria on spacecraft surfaces suggests that certain bacterial lineages persist even following rigorous quality control and cleaning practices. The majority of bacterial OTU observed as being recurrent belonged to actinobacteria and alphaproteobacteria, supporting the hypothesis that the measures of cleanliness exerted in spacecraft assembly cleanrooms (SAC) inadvertently select for the organisms which are the most fit to survive long journeys in space. PMID:22729532

Carbon and nitrogen inputs affect soil microbial community structure and function

NASA Astrophysics Data System (ADS)

Liu, X. J. A.; Mau, R. L.; Hayer, M.; Finley, B. K.; Schwartz, E.; Dijkstra, P.; Hungate, B. A.

2016-12-01

Climate change has been projected to increase energy and nutrient inputs to soils, affecting soil organic matter (SOM) decomposition (priming effect) and microbial communities. However, many important questions remain: how do labile C and/or N inputs affect priming and microbial communities? What is the relationship between them? To address these questions, we applied N (NH4NO3 ; 100 µg N g-1 wk-1), C (13C glucose; 1000 µg C g-1 wk-1), C+N to four different soils for five weeks. We found: 1) N showed no effect, whereas C induced the greatest priming, and C+N had significantly lower priming than C. 2) C and C+N additions increased the relative abundance of actinobacteria, proteobacteria, and firmicutes, but reduced relative abundance of acidobacteria, chloroflexi, verrucomicrobia, planctomycetes, and gemmatimonadetes. 3) Actinobacteria and proteobacteria increased relative abundance over time, but most others decreased over time. 4) substrate additions (N, C, C+N) significantly reduced microbial alpha diversity, which also decreased over time. 5) For beta diversity, C and C+N formed significantly different communities compare to the control and N treatments. Overtime, microbial community structure significantly altered. Four soils have drastically different community structures. These results indicate amounts of substrate C were determinant factors in modulating the rate of SOM decomposition and microbial communities. Variable responses of different microbial communities to labile C and N inputs indicate that complex relationships between priming and microbial functions. In general, we demonstrate that energy inputs can quickly accelerate SOM decomposition whereas extra N input can slow this process, though both had similar microbial community responses.

Characterization of Growing Soil Bacterial Communities across a pH gradient Using H218O DNA-Stable Isotope Probing

NASA Astrophysics Data System (ADS)

Welty-Bernard, A. T.; Schwartz, E.

2014-12-01

Recent studies have established consistent relationships between pH and bacterial diversity and community structure in soils from site-specific to landscape scales. However, these studies rely on DNA or PLFA extraction techniques from bulk soils that encompass metabolically active and inactive, or dormant, communities, and loose DNA. Dormant cells may comprise up to 80% of total live cells. If dormant cells dominate a particular environment, it is possible that previous interpretations of the soil variables assumed to drive communities could be profoundly affected. We used H218O stable isotope probing and bar-coded illumina sequencing of 16S rRNA genes to monitor the response of actively growing communities to changes in soil pH in a soil microcosm over 14 days. This substrate-independent approach has several advantages over 13C or 15N-labelled molecules in that all growing bacteria should be able to make use of water, allowing characterization of whole communities. We hypothesized that Acidobacteria would increasingly dominate the growing community and that Actinobacteria and Bacteroidetes would decline, given previously established responses by these taxa to soil pH. Instead, we observed the reverse. Actinobacteria abundance increased three-fold from 26 to 76% of the overall community as soil pH fell from pH 5.6 to pH 4.6. Shifts in community structure and decreases in diversity with declining soil pH were essentially driven by two families, Streptomyceaca and Microbacteracea, which collectively increased from 2 to 40% of the entire community. In contrast, Acidobacteria as a whole declined although numbers of subdivision 1 remained stable across all soil pH levels. We suggest that the brief incubation period in this SIP study selected for growth of acid-tolerant Actinobacteria over Acidobacteria. Taxa within Actinomycetales have been readily cultured over short time frames, suggesting rapid growth patterns. Conversely, taxa within Acidobacteria have been

Endophytic bacterial diversity in the phyllosphere of Amazon Paullinia cupana associated with asymptomatic and symptomatic anthracnose.

PubMed

Bogas, Andréa Cristina; Ferreira, Almir José; Araújo, Welington Luiz; Astolfi-Filho, Spartaco; Kitajima, Elliot Watanabe; Lacava, Paulo Teixeira; Azevedo, João Lúcio

2015-01-01

Endophytes colonize an ecological niche similar to that of phytopathogens, which make them candidate for disease suppression. Anthracnose is a disease caused by Colletotrichum spp., a phytopathogen that can infect guarana (Paullinia cupana), an important commercial crop in the Brazilian Amazon. We investigated the diversity of endophytic bacteria inhabiting the phyllosphere of asymptomatic and symptomatic anthracnose guarana plants. The PCR-denaturation gradient gel electrophoresis (PCR-DGGE) fingerprints revealed differences in the structure of the evaluated communities. Detailed analysis of endophytic bacteria composition using culture-dependent and 16S rRNA clone libraries revealed the presence of Firmicutes, Proteobacteria, Actinobacteria, Bacteroidetes, and Acidobacteria phyla. Firmicutes comprised the majority of isolates in asymptomatic plants (2.40E(-4)). However, cloning and sequencing of 16S rRNA revealed differences at the genus level for Neisseria (1.4E(-4)), Haemophilus (2.1E(-3)) and Arsenophonus (3.6E(-5)) in asymptomatic plants, Aquicella (3.5E(-3)) in symptomatic anthracnose plants, and Pseudomonas (1.1E(-3)), which was mainly identified in asymptomatic plants. In cross-comparisons of the endophytic bacterial communities as a whole, symptomatic anthracnose plants contained higher diversity, as reflected in the Shannon-Weaver and Simpson indices estimation (P < 0.05). Similarly, comparisons using LIBSHUFF and heatmap analysis for the relative abundance of operational taxonomic units (OTUs) showed differences between endophytic bacterial communities. These data are in agreement with the NMSD and ANOSIM analysis of DGGE profiles. Our results suggest that anthracnose can restructure endophytic bacterial communities by selecting certain strains in the phyllosphere of P. cupana. The understanding of these interactions is important for the development of strategies of biocontrol for Colletotrichum.

Response of Archaeal and Bacterial Soil Communities to Changes Associated with Outdoor Cattle Overwintering

PubMed Central

Chroňáková, Alica; Schloter-Hai, Brigitte; Radl, Viviane; Endesfelder, David; Quince, Christopher; Elhottová, Dana; Šimek, Miloslav; Schloter, Michael

2015-01-01

Archaea and bacteria are important drivers for nutrient transformations in soils and catalyse the production and consumption of important greenhouse gases. In this study, we investigate changes in archaeal and bacterial communities of four Czech grassland soils affected by outdoor cattle husbandry. Two show short-term (3 years; STI) and long-term impact (17 years; LTI), one is regenerating from cattle impact (REG) and a control is unaffected by cattle (CON). Cattle manure (CMN), the source of allochthonous microbes, was collected from the same area. We used pyrosequencing of 16S rRNA genes to assess the composition of archaeal and bacterial communities in each soil type and CMN. Both short- and long- term cattle impact negatively altered archaeal and bacterial diversity, leading to increase of homogenization of microbial communities in overwintering soils over time. Moreover, strong shifts in the prokaryotic communities were observed in response to cattle overwintering, with the greatest impact on archaea. Oligotrophic and acidophilic microorganisms (e.g. Thaumarchaeota, Acidobacteria, and α-Proteobacteria) dominated in CON and expressed strong negative response to increased pH, total C and N. Whereas copiotrophic and alkalophilic microbes (e.g. methanogenic Euryarchaeota, Firmicutes, Chloroflexi, Actinobacteria, and Bacteroidetes) were common in LTI showing opposite trends. Crenarchaeota were also found in LTI, though their trophic interactions remain cryptic. Firmicutes, Bacteroidetes, Methanobacteriaceae, and Methanomicrobiaceae indicated the introduction and establishment of faecal microbes into the impacted soils, while Chloroflexi and Methanosarcinaceae suggested increased abundance of soil-borne microbes under altered environmental conditions. The observed changes in prokaryotic community composition may have driven corresponding changes in soil functioning. PMID:26274496

Phylogenetic diversity of bacteria associated with Paleolithic paintings and surrounding rock walls in two Spanish caves (Llonín and La Garma).

PubMed

Schabereiter-Gurtner, Claudia; Saiz-Jimenez, Cesareo; Piñar, Guadalupe; Lubitz, Werner; Rölleke, Sabine

2004-02-01

Bacterial diversity in caves is still rarely investigated using culture-independent techniques. In the present study, bacterial communities on Paleolithic paintings and surrounding rock walls in two Spanish caves (Llonín and La Garma) were analyzed, using 16S rDNA-based denaturing gradient gel electrophoresis community fingerprinting and phylogenetic analyses without prior cultivation. Results revealed complex bacterial communities consisting of a high number of novel 16S rDNA sequence types and indicated a high biodiversity of lithotrophic and heterotrophic bacteria. Identified bacteria were related to already cultured bacteria (39 clones) and to environmental 16S rDNA clones (46 clones). The nearest phylogenetic relatives were members of the Proteobacteria (41.1%), of the Acidobacterium division (16.5%), Actinobacteria (20%), Firmicutes (10.6%), of the Cytophaga/Flexibacter/Bacteroides division (5.9%), Nitrospira group (3.5%), green non-sulfur bacteria (1.2%), and candidate WS3 division (1.2%). Thirteen of these clones were most closely related to those obtained from the previous studies on Tito Bustillo Cave. The comparison of the present data with the data obtained previously from Altamira and Tito Bustillo Caves revealed similarities in the bacterial community components, especially in the high abundance of the Acidobacteria and Rhizobiaceae, and in the presence of bacteria related to ammonia and sulfur oxidizers.

Endophytic bacterial community living in roots of healthy and 'Candidatus Phytoplasma mali'-infected apple (Malus domestica, Borkh.) trees.

PubMed

Bulgari, Daniela; Bozkurt, Adem I; Casati, Paola; Cağlayan, Kadriye; Quaglino, Fabio; Bianco, Piero A

2012-11-01

'Candidatus Phytoplasma mali', the causal agent of apple proliferation (AP) disease, is a quarantine pathogen controlled by chemical treatments against insect vectors and eradication of diseased plants. In accordance with the European Community guidelines, novel strategies should be developed for sustainable management of plant diseases by using resistance inducers (e.g. endophytes). A basic point for the success of this approach is the study of endophytic bacteria associated with plants. In the present work, endophytic bacteria living in healthy and 'Ca. Phytoplasma mali'-infected apple trees were described by cultivation-dependent and independent methods. 16S rDNA sequence analysis showed the presence of the groups Proteobacteria, Acidobacteria, Bacteroidetes, Actinobacteria, Chlamydiae, and Firmicutes. In detail, library analyses underscored 24 and 17 operational taxonomic units (OTUs) in healthy and infected roots, respectively, with a dominance of Betaproteobacteria. Moreover, differences in OTUs number and in CFU/g suggested that phytoplasmas could modify the composition of endophytic bacterial communities associated with infected plants. Intriguingly, the combination of culturing methods and cloning analysis allowed the identification of endophytic bacteria (e.g. Bacillus, Pseudomonas, and Burkholderia) that have been reported as biocontrol agents. Future research will investigate the capability of these bacteria to control 'Ca. Phytoplasma mali' in order to develop sustainable approaches for managing AP.

Plants of the fynbos biome harbour host species-specific bacterial communities.

PubMed

Miyambo, Tsakani; Makhalanyane, Thulani P; Cowan, Don A; Valverde, Angel

2016-08-01

The fynbos biome in South Africa is globally recognised as a plant biodiversity hotspot. However, very little is known about the bacterial communities associated with fynbos plants, despite interactions between primary producers and bacteria having an impact on the physiology of both partners and shaping ecosystem diversity. This study reports on the structure, phylogenetic composition and potential roles of the endophytic bacterial communities located in the stems of three fynbos plants (Erepsia anceps, Phaenocoma prolifera and Leucadendron laureolum). Using Illumina MiSeq 16S rRNA sequencing we found that different subpopulations of Deinococcus-Thermus, Alphaproteobacteria, Acidobacteria and Firmicutes dominated the endophytic bacterial communities. Alphaproteobacteria and Actinobacteria were prevalent in P. prolifera, whereas Deinococcus-Thermus dominated in L. laureolum, revealing species-specific host-bacteria associations. Although a high degree of variability in the endophytic bacterial communities within hosts was observed, we also detected a core microbiome across the stems of the three plant species, which accounted for 72% of the sequences. Altogether, it seems that both deterministic and stochastic processes shaped microbial communities. Endophytic bacterial communities harboured putative plant growth-promoting bacteria, thus having the potential to influence host health and growth. © FEMS 2016. All rights reserved. For permissions, please e-mail: journals.permissions@oup.com.

Microbial community composition and functions are resilient to metal pollution along two forest soil gradients.

PubMed

Azarbad, Hamed; Niklińska, Maria; Laskowski, Ryszard; van Straalen, Nico M; van Gestel, Cornelis A M; Zhou, Jizhong; He, Zhili; Wen, Chongqing; Röling, Wilfred F M

2015-01-01

Despite the global importance of forests, it is virtually unknown how their soil microbial communities adapt at the phylogenetic and functional level to long-term metal pollution. Studying 12 sites located along two distinct gradients of metal pollution in Southern Poland revealed that functional potential and diversity (assessed using GeoChip 4.2) were highly similar across the gradients despite drastically diverging metal contamination levels. Metal pollution level did, however, significantly impact bacterial community structure (as shown by MiSeq Illumina sequencing of 16S rRNA genes), but not bacterial taxon richness and community composition. Metal pollution caused changes in the relative abundance of specific bacterial taxa, including Acidobacteria, Actinobacteria, Bacteroidetes, Chloroflexi, Firmicutes, Planctomycetes and Proteobacteria. Also, a group of metal-resistance genes showed significant correlations with metal concentrations in soil. Our study showed that microbial communities are resilient to metal pollution; despite differences in community structure, no clear impact of metal pollution levels on overall functional diversity was observed. While screens of phylogenetic marker genes, such as 16S rRNA genes, provide only limited insight into resilience mechanisms, analysis of specific functional genes, e.g. involved in metal resistance, appears to be a more promising strategy. © FEMS 2014. All rights reserved. For permissions, please e-mail: journals.permissions@oup.com.

Effect of long-term industrial waste effluent pollution on soil enzyme activities and bacterial community composition.

PubMed

Subrahmanyam, Gangavarapu; Shen, Ju-Pei; Liu, Yu-Rong; Archana, Gattupalli; Zhang, Li-Mei

2016-02-01

Although numerous studies have addressed the influence of exogenous pollutants on microorganisms, the effect of long-term industrial waste effluent (IWE) pollution on the activity and diversity of soil bacteria was still unclear. Three soil samples characterized as uncontaminated (R1), moderately contaminated (R2), and highly contaminated (R3) receiving mixed organic and heavy metal pollutants for more than 20 years through IWE were collected along the Mahi River basin, Gujarat, western India. Basal soil respiration and in situ enzyme activities indicated an apparent deleterious effect of IWE on microbial activity and soil function. Community composition profiling of soil bacteria using 16S rRNA gene amplification and denaturing gradient gel electrophoresis (DGGE) method indicated an apparent bacterial community shift in the IWE-affected soils. Cloning and sequencing of DGGE bands revealed that the dominated bacterial phyla in polluted soil were affiliated with Firmicutes, Acidobacteria, and Actinobacteria, indicating that these bacterial phyla may have a high tolerance to pollutants. We suggested that specific bacterial phyla along with soil enzyme activities could be used as relevant biological indicators for long-term pollution assessment on soil quality. Graphical Abstract Bacterial community profiling and soil enzyme activities in long-term industrial waste effluent polluted soils.

Comparative bacterial community analysis in relatively pristine and anthropogenically influenced mangrove ecosystems on the Red Sea.

PubMed

Ullah, Riaz; Yasir, Muhammad; Khan, Imran; Bibi, Fehmida; Sohrab, Sayed Sartaj; Al-Ansari, Ahmed; Al-Abbasi, Fahad; Al-Sofyani, Abdulmohsin A; Daur, Ihsanullah; Lee, Seon-Woo; Azhar, Esam I

2017-08-01

Mangrove habitats are ecologically important ecosystems that are under severe pressure worldwide because of environmental changes and human activities. In this study, 16S rRNA gene amplicon deep-sequencing was used to compare bacterial communities in Red Sea mangrove ecosystems at anthropogenically influenced coastal sites with those at a relatively pristine island site. In total, 32 phyla were identified from the mangrove rhizospheres, with Proteobacteria predominating at each of the studied sites; however, the relative abundance was significantly decreased at the coastal sites (Mastorah, MG-MS; Ar-Rayis, MG-AR) compared with the pristine island site near Dhahban (MG-DBI). The phyla Actinobacteria, Firmicutes, Acidobacteria, Chloroflexi, Spirochetes, and Planctomycetes were present at a relative abundance of >1% at the MG-MS and MG-AR sites, but their concentration was <1% at the MG-DBI site. A total of 1659 operational taxonomic units (OTUs) were identified at the species level, and approximately 945 OTUs were shared across the different sampling sites. Multivariate principal coordinate data analysis separated the MG-DBI site from the MG-AR and MG-MS cluster. Specific bacterial taxa were enriched at each location, and in particular, the genera Pseudoalteromonas and Cobetia were predominantly identified in the MG-DBI site compared with the anthropogenically influenced coastal sites.

Ribosome reinitiation at leader peptides increases translation of bacterial proteins.

PubMed

Korolev, Semen A; Zverkov, Oleg A; Seliverstov, Alexandr V; Lyubetsky, Vassily A

2016-04-16

Short leader genes usually do not encode stable proteins, although their importance in expression control of bacterial genomes is widely accepted. Such genes are often involved in the control of attenuation regulation. However, the abundance of leader genes suggests that their role in bacteria is not limited to regulation. Specifically, we hypothesize that leader genes increase the expression of protein-coding (structural) genes via ribosome reinitiation at the leader peptide in the case of a short distance between the stop codon of the leader gene and the start codon of the structural gene. For instance, in Actinobacteria, the frequency of leader genes at a distance of 10-11 bp is about 70 % higher than the mean frequency within the 1 to 65 bp range; and it gradually decreases as the range grows longer. A pronounced peak of this frequency-distance relationship is also observed in Proteobacteria, Bacteroidetes, Spirochaetales, Acidobacteria, the Deinococcus-Thermus group, and Planctomycetes. In contrast, this peak falls to the distance of 15-16 bp and is not very pronounced in Firmicutes; and no such peak is observed in cyanobacteria and tenericutes. Generally, this peak is typical for many bacteria. Some leader genes located close to a structural gene probably play a regulatory role as well.

Bacterial communities in sediment of a Mediterranean marine protected area.

PubMed

Catania, Valentina; Sarà, Gianluca; Settanni, Luca; Quatrini, Paola

2017-04-01

Biodiversity is crucial in preservation of ecosystems, and bacterial communities play an indispensable role for the functioning of marine ecosystems. The Mediterranean marine protected area (MPA) "Capo Gallo-Isola delle Femmine" was instituted to preserve marine biodiversity. The bacterial diversity associated with MPA sediment was compared with that from sediment of an adjacent harbour exposed to intense nautical traffic. The MPA sediment showed higher diversity with respect to the impacted site. A 16S rDNA clone library of the MPA sediment allowed the identification of 7 phyla: Proteobacteria (78%), Firmicutes (11%), Acidobacteria (3%), Actinobacteria (3%), Bacteroidetes (2%), Planctomycetes (2%), and Cyanobacteria (1%). Analysis of the hydrocarbon (HC)-degrading bacteria was performed using enrichment cultures. Most of the MPA sediment isolates were affiliated with Gram-positive G+C rich bacteria, whereas the majority of taxa in the harbour sediment clustered with Alpha- and Gammaproteobacteria; no Gram-positive HC degraders were isolated from the harbour sediment. Our results show that protection probably has an influence on bacterial diversity, and suggest the importance of monitoring the effects of protection at microbial level as well. This study creates a baseline of data that can be used to assess changes over time in bacterial communities associated with a Mediterranean MPA.

Characterization of Bacterial Communities Associated with Deep-Sea Corals on Gulf of Alaska Seamounts†

PubMed Central

Penn, Kevin; Wu, Dongying; Eisen, Jonathan A.; Ward, Naomi

2006-01-01

Although microbes associated with shallow-water corals have been reported, deepwater coral microbes are poorly characterized. A cultivation-independent analysis of Alaskan seamount octocoral microflora showed that Proteobacteria (classes Alphaproteobacteria and Gammaproteobacteria), Firmicutes, Bacteroidetes, and Acidobacteria dominate and vary in abundance. More sampling is needed to understand the basis and significance of this variation. PMID:16461727

New microbes as causative agents of Ibuprofen degradation capabilities in the hyporheic zone of a lowland stream

NASA Astrophysics Data System (ADS)

Njeru, Cyrus; Posselt, Malte; Horn, Marcus A.

2017-04-01

Ibuprofen is a non-steroidal anti-inflammatory pain reliever and among pharmaceutical residues detected in aquatic environments. Widespread use of the drug and incomplete removal during waste water treatment results in its persistence in effluents and receiving waters. Potential total removal by microbial activity in the hyporheic zone (HZ) of rivers downstream of wastewater treatment plant discharge sites has been hypothesized. Ibuprofen degradation associated microbial communities in are essentially unknown. To address this hypothesis, two sets of oxic HZ sediment microcosms spiked with ibuprofen only (5, 40, 200 and 400 µM), or ibuprofen and 1 mM acetate were set up under laboratory conditions. Ibuprofen degradation in non-sterile relative to autoclaved sediments indicated removal by microbial degradation. Ibuprofen was completely consumed in the absence and presence of supplemental acetate after approximately 11 and 16 days, respectively. Refeeding of ibuprofen and acetate after the first depletion resulted in complete degradation within 24 hours in all treatments. Metabolites of ibuprofen included 1-, 2-, 3-hydroxy- and carboxyibuprofen. Quantitative real-time PCR revealed no pronounced differences in copy numbers of 16S rRNA gene or transcripts between non-spiked controls and treatments. Time resolved triplicate amplicon Illumina MiSeq sequencing targeting the 16S rRNA genes and transcripts revealed increased relative abundances of Proteobacteria, Acidobacteria, Actinobacteria and Firmicutes in treatments with compared to those without ibuprofen. Alpha-, Beta- and Deltaproteobacteria were most active as indicated by RNA based analyses. Enrichment and isolation yielded new Alphaproteobacteria utilizing ibuprofen as sole carbon and energy source. The collective results indicated that (i) HZ sediments sustain efficient biotic (micro-)pollutant removal and (ii) are a reservoir of hitherto unknown microbial diversity associated with such ecosystem services

Chloromuconolactone dehalogenase ClcF of actinobacteria.

PubMed

Solyanikova, Inna P; Plotnikova, Elena G; Shumkova, Ekaterina S; Robota, Irina V; Prisyazhnaya, Natalya V; Golovleva, Ludmila A

2014-01-01

This work investigated the distribution of the clcF gene in actinobacteria isolated from different ecotopes. The gene encodes chloromuconolactone dehalogenase (CMLD) ClcF, the enzyme found to date in only one representative of Gram-positive bacteria, Rhodococcus opacus 1CP, adapted to 2-chlorophenol (2CP). Using primers specific to the clcF gene, from the DNA matrix of rhodococcal strains closely related to species Rhodococcus wratislaviensis (P1, P12, P13, P20, G10, KT112, KT723, BO1) we obtained PCR products whose nucleotide sequences were 100% identical to that of the clcF gene from strain R. opacus 1CP. CMLDs isolated from the biomass of strains Rhodococcus spp. G10 and P1 grown on 2CP did not differ by their subunit molecular mass deduced from the known amino acid sequence of the clcF gene from the ClcF of strain R. opacus 1CP. Matrix-assisted laser dissociation/ionization time-of-flight mass spectrometry showed the presence of a peak with m/z 11,194-11,196 Da both in whole cells and in protein solutions with a ClcF activity. Thus, we have first time shown the distribution of ClcF among actinobacteria isolated from geographically distant habitats.

Bioprospecting Deep-Sea Actinobacteria for Novel Anti-infective Natural Products

PubMed Central

Xu, Dongbo; Han, Linna; Li, Chunhui; Cao, Qi; Zhu, Duolong; Barrett, Nolan H.; Harmody, Dedra; Chen, Jing; Zhu, Haining; McCarthy, Peter J.; Sun, Xingmin; Wang, Guojun

2018-01-01

The global prevalence of drug resistance has created an urgent need for the discovery of novel anti-infective drugs. The major source of antibiotics in current clinical practice is terrestrial actinobacteria; the less-exploited deep-sea actinobacteria may serve as an unprecedented source of novel natural products. In this study, we evaluated 50 actinobacteria strains derived from diverse deep water sponges and environmental niches for their anti-microbial activities against a panel of pathogens including Candida albicans, Clostridium difficile, Staphylococcus aureus, and methicillin-resistant S. aureus (MRSA), and Pseudomonas aeruginosa. More than half of the tested strains (27) were identified as active in at least one assay. The rare earth salt lanthanum chloride (LaCl3) was shown to be as an effective elicitor. Among the 27 strains, the anti-microbial activity of 15 were induced or enhanced by the addition of LaCl3. This part of study focused on one strain R818, in which potent antifungal activity was induced by the addition of LaCl3. We found that the LaCl3-activated metabolites in R818 are likely antimycin-type compounds. One of them, compound 1, has been purified. Spectroscopic analyses including HR-MS and 1D NMR indicated that this compound is urauchimycin D. The antifungal activity of compound 1 was confirmed with a minimal inhibitory concentration (MIC) of 25 μg/mL; the purified compound also showed a moderate activity against C. difficile. Additional notable strains are: strain N217 which showed both antifungal and antibacterial (including P. aeruginosa) activities and strain M864 which showed potent activity against C. difficile with an MIC value (0.125 μg/mL) lower than those of vancomycin and metronidazole. Our preliminary studies show that deep-sea actinobacteria is a promising source of anti-infective natural products. PMID:29760684

The rhizospheres of traditional medicinal plants in Panxi, China, host a diverse selection of actinobacteria with antimicrobial properties.

PubMed

Zhao, Ke; Penttinen, Petri; Chen, Qiang; Guan, Tongwei; Lindström, Kristina; Ao, Xiaoling; Zhang, Lili; Zhang, Xiaoping

2012-06-01

Actinobacteria are a prolific source of antibiotics. Since the rate of discovery of novel antibiotics is decreasing, actinobacteria from unique environments need to be explored. In particular, actinobacterial biocontrol strains from medicinal plants need to be studied as they can be a source of potent antibiotics. We combined culture-dependent and culture-independent methods in analyzing the actinobacterial diversity in the rhizosphere of seven traditional medicinal plant species from Panxi, China, and assessed the antimicrobial activity of the isolates. Each of the plant species hosted a unique set of actinobacterial strains. Out of the 64 morphologically distinct isolates, half were Streptomyces sp., eight were Micromonospora sp., and the rest were members of 18 actinobacterial genera. In particular, Ainsliaea henryi Diels. hosted a diverse selection of actinobacteria, although the 16S ribosomal RNA (rRNA) sequence identity ranges of the isolates and of the 16S rRNA gene clone library were not congruent. In the clone library, 40% of the sequences were related to uncultured actinobacteria, emphasizing the need to develop isolation methods to assess the full potential of the actinobacteria. All Streptomyces isolates showed antimicrobial activity. While the antimicrobial activities of the rare actinobacteria were limited, the growth of Escherichia coli, Verticillium dahliae, and Fusarium oxysporum were inhibited only by rare actinobacteria, and strains related to Saccharopolyspora shandongensis and Streptosporangium roseum showed broad antimicrobial activity.

Polysaccharide utilization loci and nutritional specialization in a dominant group of butyrate-producing human colonic Firmicutes.

PubMed

Sheridan, Paul O; Martin, Jennifer C; Lawley, Trevor D; Browne, Hilary P; Harris, Hugh M B; Bernalier-Donadille, Annick; Duncan, Sylvia H; O'Toole, Paul W; Scott, Karen P; Flint, Harry J

2016-02-01

Firmicutes and Bacteroidetes are the predominant bacterial phyla colonizing the healthy human large intestine. Whilst both ferment dietary fibre, genes responsible for this important activity have been analysed only in the Bacteroidetes , with very little known about the Firmicutes . This work investigates the carbohydrate-active enzymes (CAZymes) in a group of Firmicutes , Roseburia spp. and Eubacterium rectale , which play an important role in producing butyrate from dietary carbohydrates and in health maintenance. Genome sequences of 11 strains representing E. rectale and four Roseburia spp. were analysed for carbohydrate-active genes. Following assembly into a pan-genome, core, variable and unique genes were identified. The 1840 CAZyme genes identified in the pan-genome were assigned to 538 orthologous groups, of which only 26 were present in all strains, indicating considerable inter-strain variability. This analysis was used to categorize the 11 strains into four carbohydrate utilization ecotypes (CUEs), which were shown to correspond to utilization of different carbohydrates for growth. Many glycoside hydrolase genes were found linked to genes encoding oligosaccharide transporters and regulatory elements in the genomes of Roseburia spp. and E. rectale , forming distinct polysaccharide utilization loci (PULs). Whilst PULs are also a common feature in Bacteroidetes , key differences were noted in these Firmicutes , including the absence of close homologues of Bacteroides polysaccharide utilization genes, hence we refer to Gram-positive PULs (gpPULs). Most CAZyme genes in the Roseburia / E. rectale group are organized into gpPULs. Variation in gpPULs can explain the high degree of nutritional specialization at the species level within this group.

Polysaccharide utilization loci and nutritional specialization in a dominant group of butyrate-producing human colonic Firmicutes

PubMed Central

O. Sheridan, Paul; Martin, Jennifer C.; Lawley, Trevor D.; Browne, Hilary P.; Harris, Hugh M. B.; Bernalier-Donadille, Annick; Duncan, Sylvia H.; O'Toole, Paul W.; J. Flint, Harry

2016-01-01

Firmicutes and Bacteroidetes are the predominant bacterial phyla colonizing the healthy human large intestine. Whilst both ferment dietary fibre, genes responsible for this important activity have been analysed only in the Bacteroidetes, with very little known about the Firmicutes. This work investigates the carbohydrate-active enzymes (CAZymes) in a group of Firmicutes, Roseburia spp. and Eubacterium rectale, which play an important role in producing butyrate from dietary carbohydrates and in health maintenance. Genome sequences of 11 strains representing E. rectale and four Roseburia spp. were analysed for carbohydrate-active genes. Following assembly into a pan-genome, core, variable and unique genes were identified. The 1840 CAZyme genes identified in the pan-genome were assigned to 538 orthologous groups, of which only 26 were present in all strains, indicating considerable inter-strain variability. This analysis was used to categorize the 11 strains into four carbohydrate utilization ecotypes (CUEs), which were shown to correspond to utilization of different carbohydrates for growth. Many glycoside hydrolase genes were found linked to genes encoding oligosaccharide transporters and regulatory elements in the genomes of Roseburia spp. and E. rectale, forming distinct polysaccharide utilization loci (PULs). Whilst PULs are also a common feature in Bacteroidetes, key differences were noted in these Firmicutes, including the absence of close homologues of Bacteroides polysaccharide utilization genes, hence we refer to Gram-positive PULs (gpPULs). Most CAZyme genes in the Roseburia/E. rectale group are organized into gpPULs. Variation in gpPULs can explain the high degree of nutritional specialization at the species level within this group. PMID:28348841

Isolation, structure elucidation and anticancer activity from Brevibacillus brevis EGS 9 that combats Multi Drug Resistant actinobacteria.

PubMed

Arumugam, T; Senthil Kumar, P; Hemavathy, R V; Swetha, V; Karishma Sri, R

2018-02-01

Actinobacteria is the most widely distributed organism in the mangrove environment and produce a large amount of secondary metabolites. A new environmental actinobacterial stain exhibited strong antimicrobial activity against vancomycin and methicillin resistant actinobacteria. The active producer strain was found to be as Brevibacillus brevis EGS9, which was confirmed by its morphological, biochemical characteristics and 16S rRNA gene sequencing. It was deposited in NCBI GeneBank database and received with an accession number of KX388147. Brevibacillus brevis EGS9 was cultivated by submerged fermentation to produce antimicrobial compounds. The anti-proliferative agent was extracted from Brevibacillus brevis EGS9 with ethyl acetate. The bioactive metabolites of mangrove actinobacteria was identified by Liquid chromatography with mass spectrometry analysis. The result of the present investigation revealed that actinobacteria isolated from mangroves are potent source of anticancer activity. The strain of Brevibacillus brevis EGS9 exhibited a potential in vitro anticancer activity. The present research concluded that the actinobacteria isolated from mangrove soil sediment are valuable in discovery of novel species. Copyright © 2017. Published by Elsevier Ltd.

Actinobacteria and Myxobacteria-Two of the Most Important Bacterial Resources for Novel Antibiotics.

PubMed

Landwehr, Wiebke; Wolf, Corinna; Wink, Joachim

Bacteria have been by far the most promising resource for antibiotics in the past decades and will in all undoubtedly remain an important resource of innovative bioactive natural products in the future. Actinobacteria have been screened for many years, whereas the Myxobacteria have been underestimated in the past. Even though Actinobacteria belong to the Gram-positive and Myxobacteria to the Gram-negative bacteria both groups have a number of similar characters, as they both have huge genomes with in some cases more than 10kB and a high GC content and they both can differentiate and have often cell cycles including the formation of spores. Actinobacteria have been used for the antibiotic research for many years, hence it is often discussed whether this resource has now been exhaustively exploited but most of the screening programs from pharmaceutical companies were basing on the cultivation mainly of members of the genus Streptomyces or Streptomyces like strains (e.g., some Saccharopolyspora, Amycolatopsis or Actinomadura species) by use of standard methods so that many of the so called "neglected" Actinobacteria were overlooked the whole time. The present review gives an overview on the state of the art regarding new bioactive compounds with a focus on the marine habitats. Furthermore, the evaluation of Myxobacteria in our ongoing search for novel anti-infectives is highlighted.

Unexpected Stability of Bacteroidetes and Firmicutes Communities in Laboratory Biogas Reactors Fed with Different Defined Substrates

PubMed Central

Ratering, S.; Kramer, I.; Schmidt, M.; Zerr, W.; Schnell, S.

2012-01-01

In the present study, bacterial communities in 200-liter biogas reactors containing liquid manure consecutively fed with casein, starch, and cream were investigated over a period of up to 33 days. A 16S rRNA gene clone library identified Bacteroidetes and Firmicutes as the most abundant bacterial groups in the starting material, at 58.9% and 30.1% of sequences, respectively. The community development of both groups was monitored by real-time PCR and single-strand conformation polymorphism (SSCP) analysis. The Firmicutes and Bacteroidetes communities were unexpectedly stable and hardly influenced by batch-feeding events. The continuous feeding of starch led to community shifts that nevertheless contributed to a stable reactor performance. A longer starving period and a change in the pH value resulted in further community shifts within the Bacteroidetes but did not influence the Firmicutes. Predominant DNA bands from SSCP gels were cloned and sequenced. Sequences related to Peptococcaceae, Cytophagales, and Petrimonas sulfuriphila were found in all samples from all experiments. Real-time PCR demonstrated the abundance of members of the phylum Bacteroidetes and also reflected changes in gene copy numbers in conjunction with a changing pH value and acetate accumulation. PMID:22247168

Genomes of planktonic Acidimicrobiales: widening horizons for marine Actinobacteria by metagenomics.

PubMed

Mizuno, Carolina Megumi; Rodriguez-Valera, Francisco; Ghai, Rohit

2015-02-10

The genomes of four novel marine Actinobacteria have been assembled from large metagenomic data sets derived from the Mediterranean deep chlorophyll maximum (DCM). These are the first marine representatives belonging to the order Acidimicrobiales and only the second group of planktonic marine Actinobacteria to be described. Their streamlined genomes and photoheterotrophic lifestyle suggest that they are planktonic, free-living microbes. A novel rhodopsin clade, acidirhodopsins, related to freshwater actinorhodopsins, was found in these organisms. Their genomes suggest a capacity to assimilate C2 compounds, some using the glyoxylate bypass and others with the ethylmalonyl-coenzyme A (CoA) pathway. They are also able to derive energy from dimethylsulfopropionate (DMSP), sulfonate, and carbon monoxide oxidation, all commonly available in the marine habitat. These organisms appear to be prevalent in the deep photic zone at or around the DCM. The presence of sister clades to the marine Acidimicrobiales in freshwater aquatic habitats provides a new example of marine-freshwater transitions with potential evolutionary insights. Despite several studies showing the importance and abundance of planktonic Actinobacteria in the marine habitat, a representative genome was only recently described. In order to expand the genomic repertoire of marine Actinobacteria, we describe here the first Acidimicrobidae genomes of marine origin and provide insights about their ecology. They display metabolic versatility in the acquisition of carbon and appear capable of utilizing diverse sources of energy. One of the genomes harbors a new kind of rhodopsin related to the actinorhodopsin clade of freshwater origin that is widespread in the oceans. Our data also support their preference to inhabit the deep chlorophyll maximum and the deep photic zone. This work contributes to the perception of marine actinobacterial groups as important players in the marine environment with distinct and

Characterization of Thermostable Cellulases Produced by Bacillus and Geobacillus Strains

USDA-ARS?s Scientific Manuscript database

Bacterial community composition of thermophilic (60 deg C) mixed cellulose-enrichment cultures was examined by constructing a 16S rDNA clone library which demonstrated major lineages affiliated to Actinobacteria, Bacteroidetes, Chloroflexi, Deinococcus-Thermus, Firmicutes, and Proteobacteria. A tot...

Predominance of Viable Spore-Forming Piezophilic Bacteria in High-Pressure Enrichment Cultures from ~1.5 to 2.4 km-Deep Coal-Bearing Sediments below the Ocean Floor

PubMed Central

Fang, Jiasong; Kato, Chiaki; Runko, Gabriella M.; Nogi, Yuichi; Hori, Tomoyuki; Li, Jiangtao; Morono, Yuki; Inagaki, Fumio

2017-01-01

Phylogenetically diverse microorganisms have been observed in marine subsurface sediments down to ~2.5 km below the seafloor (kmbsf). However, very little is known about the pressure-adapted and/or pressure-loving microorganisms, the so called piezophiles, in the deep subseafloor biosphere, despite that pressure directly affects microbial physiology, metabolism, and biogeochemical processes of carbon and other elements in situ. In this study, we studied taxonomic compositions of microbial communities in high-pressure incubated sediment, obtained during the Integrated Ocean Drilling Program (IODP) Expedition 337 off the Shimokita Peninsula, Japan. Analysis of 16S rRNA gene-tagged sequences showed that members of spore-forming bacteria within Firmicutes and Actinobacteria were predominantly detected in all enrichment cultures from ~1.5 to 2.4 km-deep sediment samples, followed by members of Proteobacteria, Acidobacteria, and Bacteroidetes according to the sequence frequency. To further study the physiology of the deep subseafloor sedimentary piezophilic bacteria, we isolated and characterized two bacterial strains, 19R1-5 and 29R7-12, from 1.9 and 2.4 km-deep sediment samples, respectively. The isolates were both low G+C content, gram-positive, endospore-forming and facultative anaerobic piezophilic bacteria, closely related to Virgibacillus pantothenticus and Bacillus subtilis within the phylum Firmicutes, respectively. The optimal pressure and temperature conditions for growth were 20 MPa and 42°C for strain 19R1-5, and 10 MPa and 43°C for strain 29R7-12. Bacterial (endo)spores were observed in both the enrichment and pure cultures examined, suggesting that these piezophilic members were derived from microbial communities buried in the ~20 million-year-old coal-bearing sediments after the long-term survival as spores and that the deep biosphere may host more abundant gram-positive spore-forming bacteria and their spores than hitherto recognized. PMID:28220112

Predominance of Viable Spore-Forming Piezophilic Bacteria in High-Pressure Enrichment Cultures from ~1.5 to 2.4 km-Deep Coal-Bearing Sediments below the Ocean Floor.

PubMed

Fang, Jiasong; Kato, Chiaki; Runko, Gabriella M; Nogi, Yuichi; Hori, Tomoyuki; Li, Jiangtao; Morono, Yuki; Inagaki, Fumio

2017-01-01

Phylogenetically diverse microorganisms have been observed in marine subsurface sediments down to ~2.5 km below the seafloor (kmbsf). However, very little is known about the pressure-adapted and/or pressure-loving microorganisms, the so called piezophiles, in the deep subseafloor biosphere, despite that pressure directly affects microbial physiology, metabolism, and biogeochemical processes of carbon and other elements in situ . In this study, we studied taxonomic compositions of microbial communities in high-pressure incubated sediment, obtained during the Integrated Ocean Drilling Program (IODP) Expedition 337 off the Shimokita Peninsula, Japan. Analysis of 16S rRNA gene-tagged sequences showed that members of spore-forming bacteria within Firmicutes and Actinobacteria were predominantly detected in all enrichment cultures from ~1.5 to 2.4 km-deep sediment samples, followed by members of Proteobacteria, Acidobacteria, and Bacteroidetes according to the sequence frequency. To further study the physiology of the deep subseafloor sedimentary piezophilic bacteria, we isolated and characterized two bacterial strains, 19R1-5 and 29R7-12, from 1.9 and 2.4 km-deep sediment samples, respectively. The isolates were both low G+C content, gram-positive, endospore-forming and facultative anaerobic piezophilic bacteria, closely related to Virgibacillus pantothenticus and Bacillus subtilis within the phylum Firmicutes, respectively. The optimal pressure and temperature conditions for growth were 20 MPa and 42°C for strain 19R1-5, and 10 MPa and 43°C for strain 29R7-12. Bacterial (endo)spores were observed in both the enrichment and pure cultures examined, suggesting that these piezophilic members were derived from microbial communities buried in the ~20 million-year-old coal-bearing sediments after the long-term survival as spores and that the deep biosphere may host more abundant gram-positive spore-forming bacteria and their spores than hitherto recognized.

Microbiome dynamic modulation through functional diets based on pre- and probiotics (mannan-oligosaccharides and Saccharomyces cerevisiae) in juvenile rainbow trout (Oncorhynchus mykiss).

PubMed

Gonçalves, A T; Gallardo-Escárate, C

2017-05-01

This study used high-throughput sequencing to evaluate the intestinal microbiome dynamics in rainbow trout (Oncorhynchus mykiss) fed commercial diets supplemented with either pre- or probiotics (0·6% mannan-oligosaccharides and 0·5% Saccharomyces cerevisiae respectively) or the mixture of both. A total of 57 fish whole intestinal mucosa and contents bacterial communities were characterized by high-throughput sequencing and analysis of the V3-V4 region of the 16S rRNA gene, as well as the relationship between plasma biochemical health indicators and microbiome diversity. This was performed at 7, 14 and 30 days after start feeding functional diets, and microbiome diversity increased when fish fed functional diets after 7 days and it was positively correlated with plasma cholesterol levels. Dominant phyla were, in descending order, Proteobacteria, Firmicutes, Actinobacteria, Acidobacteria, Bacteroidetes and Fusobacteria. However, functional diets reduced the abundance of Gammaproteobacteria to favour abundances of organisms from Firmicutes and Fusobacteria, two phyla with members that confer beneficial effects. A dynamic shift of the microbiome composition was observed with changes after 7 days of feeding and the modulation by functional diets tend to cluster the corresponding groups apart from CTRL group. The core microbiome showed an overall stability with functional diets, except genus such as Escherichia-Shigella that suffered severe reductions on their abundances when feeding any of the functional diets. Functional diets based on pre- or probiotics dynamically modulate intestinal microbiota of juvenile trout engaging taxonomical abundance shifts that might impact fish physiological performance. This study shows for the first time the microbiome modulation dynamics by functional diets based on mannan-oligosaccharides and S. cerevisiae and their synergy using culture independent high-throughput sequencing technology, revealing the complexity behind the dietary

Pediatric obesity is associated with an altered gut microbiota and discordant shifts in Firmicutes populations.

PubMed

Riva, Alessandra; Borgo, Francesca; Lassandro, Carlotta; Verduci, Elvira; Morace, Giulia; Borghi, Elisa; Berry, David

2017-01-01

An altered gut microbiota has been linked to obesity in adulthood, although little is known about childhood obesity. The aim of this study was to characterize the composition of the gut microbiota in obese (n = 42) and normal-weight (n = 36) children aged 6 to 16. Using 16S rRNA gene-targeted sequencing, we evaluated taxa with differential abundance according to age- and sex-normalized body mass index (BMI z-score). Obesity was associated with an altered gut microbiota characterized by elevated levels of Firmicutes and depleted levels of Bacteroidetes. Correlation network analysis revealed that the gut microbiota of obese children also had increased correlation density and clustering of operational taxonomic units (OTUs). Members of the Bacteroidetes were generally better predictors of BMI z-score and obesity than Firmicutes, which was likely due to discordant responses of Firmicutes OTUs. In accordance with these observations, the main metabolites produced by gut bacteria, short chain fatty acids (SCFAs), were higher in obese children, suggesting elevated substrate utilisation. Multiple taxa were correlated with SCFA levels, reinforcing the tight link between the microbiota, SCFAs and obesity. Our results suggest that gut microbiota dysbiosis and elevated fermentation activity may be involved in the etiology of childhood obesity. © 2016 The Authors. Environmental Microbiology published by Society for Applied Microbiology and John Wiley & Sons Ltd.

Phylogenetic diversity of actinobacteria associated with soft coral Alcyonium gracllimum and stony coral Tubastraea coccinea in the East China Sea.

PubMed

Yang, Shan; Sun, Wei; Tang, Cen; Jin, Liling; Zhang, Fengli; Li, Zhiyong

2013-07-01

Actinobacteria are widely distributed in the marine environment. To date, few studies have been performed to explore the coral-associated Actinobacteria, and little is known about the diversity of coral-associated Actinobacteria. In this study, the actinobacterial diversity associated with one soft coral Alcyonium gracllimum and one stony coral Tubastraea coccinea collected from the East China Sea was investigated using both culture-independent and culture-dependent approaches. A total of 19 actinobacterial genera were detected in these two corals, among which nine genera (Corynebacterium, Dietzia, Gordonia, Kocuria, Microbacterium, Micrococcus, Mycobacterium, Streptomyces, and Candidatus Microthrix) were common, three genera (Cellulomonas, Dermatophilus, and Janibacter) were unique to the soft coral, and seven genera (Brevibacterium, Dermacoccus, Leucobacter, Micromonospora, Nocardioides, Rhodococcus, and Serinicoccus) were unique to the stony coral. This finding suggested that highly diverse Actinobacteria were associated with different types of corals. In particular, five actinobacterial genera (Cellulomonas, Dermacoccus, Gordonia, Serinicoccus, and Candidatus Microthrix) were recovered from corals for the first time, extending the known diversity of coral-associated Actinobacteria. This study shows that soft and stony corals host diverse Actinobacteria and can serve as a new source of marine actinomycetes.

Insights on the Effects of Heat Pretreatment, pH, and Calcium Salts on Isolation of Rare Actinobacteria from Karstic Caves

PubMed Central

Fang, Bao-Zhu; Salam, Nimaichand; Han, Ming-Xian; Jiao, Jian-Yu; Cheng, Juan; Wei, Da-Qiao; Xiao, Min; Li, Wen-Jun

2017-01-01

The phylum Actinobacteria is one of the most ubiquitously present bacterial lineages on Earth. In the present study, we try to explore the diversity of cultivable rare Actinobacteria in Sigangli Cave, Yunnan, China by utilizing a combination of different sample pretreatments and under different culture conditions. Pretreating the samples under different conditions of heat, setting the isolation condition at different pHs, and supplementation of media with different calcium salts were found to be effective for isolation of diverse rare Actinobacteria. During our study, a total of 204 isolates affiliated to 30 genera of phylum Actinobacteria were cultured. Besides the dominant Streptomyces, rare Actinobacteria of the genera Actinocorallia, Actinomadura, Agromyces, Alloactinosynnema, Amycolatopsis, Beutenbergia, Cellulosimicrobium, Gordonia, Isoptericola, Jiangella, Knoellia, Kocuria, Krasilnikoviella, Kribbella, Microbacterium, Micromonospora, Mumia, Mycobacterium, Nocardia, Nocardioides, Nocardiopsis, Nonomuraea, Oerskovia, Pseudokineococcus, Pseudonocardia, Rhodococcus, Saccharothrix, Streptosporangium, and Tsukamurella were isolated from these cave samples. PMID:28848538

Characterization of Bacterial Communities in Selected Smokeless Tobacco Products Using 16S rDNA Analysis

PubMed Central

Tyx, Robert E.; Stanfill, Stephen B.; Keong, Lisa M.; Rivera, Angel J.; Satten, Glen A.; Watson, Clifford H.

2016-01-01

The bacterial communities present in smokeless tobacco (ST) products have not previously reported. In this study, we used Next Generation Sequencing to study the bacteria present in U.S.-made dry snuff, moist snuff and Sudanese toombak. Sample diversity and taxonomic abundances were investigated in these products. A total of 33 bacterial families from four phyla, Actinobacteria, Firmicutes, Proteobacteria and Bacteroidetes, were identified. U.S.-produced dry snuff products contained a diverse distribution of all four phyla. Moist snuff products were dominated by Firmicutes. Toombak samples contained mainly Actinobacteria and Firmicutes (Aerococcaceae, Enterococcaceae, and Staphylococcaceae). The program PICRUSt (Phylogenetic Investigation of Communities by Reconstruction of Unobserved States) was used to impute the prevalence of genes encoding selected bacterial toxins, antibiotic resistance genes and other pro-inflammatory molecules. PICRUSt also predicted the presence of specific nitrate reductase genes, whose products can contribute to the formation of carcinogenic nitrosamines. Characterization of microbial community abundances and their associated genomes gives us an indication of the presence or absence of pathways of interest and can be used as a foundation for further investigation into the unique microbiological and chemical environments of smokeless tobacco products. PMID:26784944

Date palm and the activated sludge co-composting actinobacteria sanitization potential.

PubMed

El Fels, Loubna; Hafidi, Mohamed; Ouhdouch, Yedir

2016-01-01

The objective of this study was to find a connection between the development of the compost actinobacteria and the potential involvement of antagonistic thermophilic actinomycetes in compost sanitization as high temperature additional role. An abundance of actinobacteria and coliforms during the activated sludge and date palm co-composting is determined. Hundred actinomycete isolates were isolated from the sample collected at different composting times. To evaluate the antagonistic effects of the different recovered actinomycete isolates, several wastewater-linked microorganisms known as human and plant potential pathogens were used. The results showed that 12 isolates have an in vitro inhibitory effect on at least 9 of the indicator microorganisms while only 4 active strains inhibit all these pathogens. The antimicrobial activities of sterilized composting time extracts are also investigated.

Inner Plant Values: Diversity, Colonization and Benefits from Endophytic Bacteria

PubMed Central

Liu, Hongwei; Carvalhais, Lilia C.; Crawford, Mark; Singh, Eugenie; Dennis, Paul G.; Pieterse, Corné M. J.; Schenk, Peer M.

2017-01-01

One of the most exciting scientific advances in recent decades has been the realization that the diverse and immensely active microbial communities are not only ‘passengers’ with plants, but instead play an important role in plant growth, development and resistance to biotic and abiotic stresses. A picture is emerging where plant roots act as ‘gatekeepers’ to screen soil bacteria from the rhizosphere and rhizoplane. This typically results in root endophytic microbiome dominated by Proteobacteria, Actinobacteria and to a lesser extent Bacteroidetes and Firmicutes, but Acidobacteria and Gemmatimonadetes being almost depleted. A synthesis of available data suggest that motility, plant cell-wall degradation ability and reactive oxygen species scavenging seem to be crucial traits for successful endophytic colonization and establishment of bacteria. Recent studies provide solid evidence that these bacteria serve host functions such as improving of plant nutrients through acquisition of nutrients from soil and nitrogen fixation in leaves. Additionally, some endophytes can engage ‘priming’ plants which elicit a faster and stronger plant defense once pathogens attack. Due to these plant growth-promoting effects, endophytic bacteria are being widely explored for their use in the improvement of crop performance. Updating the insights into the mechanism of endophytic bacterial colonization and interactions with plants is an important step in potentially manipulating endophytic bacteria/microbiome for viable strategies to improve agricultural production. PMID:29312235

Metagenomic analyses of the dominant bacterial community in the Fildes Peninsula, King George Island (South Shetland Islands)

NASA Astrophysics Data System (ADS)

Foong, Choon Pin; Wong Vui Ling, Clemente Michael; González, Marcelo

2010-08-01

There is little information on the bacterial diversity of the Fildes Peninsula, King George Island. Hence, this study was conducted to determine the bacterial population of sediments and soils from the lakes, river, glacier and an abandoned oil tank area in the Fildes Peninsula, using a metagenomic approach. DNA was extracted from the sediment and soil samples, and analyzed using the 16S rDNA polymerase chain reaction-denaturing gradient gel electrophoresis (PCR-DGGE). A total of 299 DNA fragments resolved using the DGGE were sequenced. The results of the analysis provided an overview of the predominant groups of bacteria and the diversity of the bacterial communities. The most abundant phyla of bacteria in Fildes Peninsula were Bacteroidetes, Proteobacteria, Acidobacteria, Gemmatimonadetes, Nitrospira, Firmicutes, Actinobacteria, Chloroflexi, Cyanobacteria, Spirochaetes, Deinococcus-Thermus, WS3 and BRC1. All of the sediment samples from the lakes had different representatives of dominant bacterial species. Interestingly, 15% of the operational taxonomic units (OTUs) did not group into any of the existing phyla in the Ribosomal Database Project (RDP). One of the OTUs had a similarity of <0.90 when compared to the GenBank sequences and probably was a novel bacterium specific to that location. The majority of the bacterial 16S rDNA sequences were found to be closely related to those found elsewhere.

Surfactants selectively reallocated the bacterial distribution in soil bioelectrochemical remediation of petroleum hydrocarbons.

PubMed

Li, Xiaojing; Zhao, Qian; Wang, Xin; Li, Yongtao; Zhou, Qixing

2018-02-15

Soil contaminated by aged petroleum hydrocarbons is faced with scarcity of electron acceptors, low activity of functional microbes and inefficient electron transfer, which hinder the bioremediation application. The soil microbial fuel cell (MFC) simultaneously solves these problems with bioelectricity production. In this study, five types of surfactants were introduced to enhance the bioavailability of aged petroleum hydrocarbon in soils. The ampholytic surfactant (lecithos) was optimal due to the highest bioelectricity generation (0.321Cd -1 g -1 ) and promoted hydrocarbon degradation (328%), while the nonionic (glyceryl monostearate) and cationic (cetyltrimethylammonium bromide) surfactants were inefficient. The surfactants induced a special microbial enrichment affiliated with Proteobacteria, Firmicutes, Bacteroidetes, Actinobacteria, Chloroflexi, Planctomycetes and Acidobacteria (93%-99% of total) in soil MFCs. The anionic surfactant (sodium dodecyl sulfate) exhibited the strongest selectivity, and α-proteobacteria and γ-proteobacteria abundances decreased while Clostridia increased, much like the result obtained with the biosurfactant β-cyclodextrin. Furthermore, Bacillus abundance was increased in connected soil MFCs, except addition of lecithos in which Clostridium increased to 14.88% from 3.61% in the control. The high correlations among Bacillus, Phenylobacterium, Solibacillus (0.9162-0.9577) and among Alcaligenes, Dysgonomonas, Sedimentibacter (0.9538-0.9966) indicated a metabolic network of microorganisms in the soil bioelectrochemical remediation system. Copyright © 2017 Elsevier B.V. All rights reserved.

Environmental drivers of soil microbial community distribution at the Koiliaris Critical Zone Observatory.

PubMed

Tsiknia, Myrto; Paranychianakis, Nikolaos V; Varouchakis, Emmanouil A; Moraetis, Daniel; Nikolaidis, Nikolaos P

2014-10-01

Data on soil microbial community distribution at large scales are limited despite the important information that could be drawn with regard to their function and the influence of environmental factors on nutrient cycling and ecosystem services. This study investigates the distribution of Archaea, Bacteria and Fungi as well as the dominant bacterial phyla (Acidobacteria, Actinobacteria, Bacteroidetes, Firmicutes), and classes of Proteobacteria (Alpha- and Betaproteobacteria) across the Koiliaris watershed by qPCR and associate them with environmental variables. Predictive maps of microorganisms distribution at watershed scale were generated by co-kriging, using the most significant predictors. Our findings showed that 31-79% of the spatial variation in microbial taxa abundance could be explained by the parameters measured, with total organic carbon and pH being identified as the most important. Moreover, strong correlations were set between microbial groups and their inclusion on variance explanation improved the prediction power of the models. The spatial autocorrelation of microbial groups ranged from 309 to 2.226 m, and geographic distance, by itself, could explain a high proportion of their variation. Our findings shed light on the factors shaping microbial communities at a high taxonomic level and provide evidence for ecological coherence and syntrophic interactions at the watershed scale. © 2014 Federation of European Microbiological Societies. Published by John Wiley & Sons Ltd. All rights reserved.

The microbial community characteristics of ancient painted sculptures in Maijishan Grottoes, China

PubMed Central

He, Dongpeng; Gu, Ji-Dong; Feng, Huyuan; Chen, Tuo; Liu, Guangxiu; An, Lizhe

2017-01-01

In this study, a culture-independent Illumina MiSeq sequencing strategy was applied to investigate the microbial communities colonizing the ancient painted sculptures of the Maijishan Grottoes, a famous World Cultural Heritage site listed by UNESCO in China. Four mixed samples were collected from Cave 4–4 of the Maijishan Grottoes, the so-called Upper Seven Buddha Pavilion, which was built during the Northern Zhou Dynasty (557-581AD). The 16/18S rRNA gene-based sequences revealed a rich bacterial diversity and a relatively low fungal abundance, including the bacterial groups Actinobacteria, Acidobacteria, Bacteroidetes, Cyanobacteria, Chloroflexi, Firmicutes, Proteobacteria and Verrucomicrobia and the fungal groups Ascomycota, Basidiomycota and Chytridiomycota. Among them, the bacteria genera of Pseudonocardia and Rubrobacter and unclassified fungi in the order of Capnodiales were dominant. The relative abundance of Pseudonocardia in the painted layer samples was higher than that in the dust sample, while Cyanobacteria dominated in the dust sample. Many of them have been discovered at other cultural heritage sites and associated with the biodeterioration of cultural relics. The presence and activity of these pioneering microorganisms may lead to an unexpected deterioration of the painted sculptures that are preserved in this heritage site. Thus, proper management strategies and potential risk monitoring should be used in the Maijishan Grottoes to improve the conservation of these precious painted sculptures. PMID:28678844

Responses of bacterial community structure and denitrifying bacteria in biofilm to submerged macrophytes and nitrate

NASA Astrophysics Data System (ADS)

Zhang, Songhe; Pang, Si; Wang, Peifang; Wang, Chao; Guo, Chuan; Addo, Felix Gyawu; Li, Yi

2016-10-01

Submerged macrophytes play important roles in constructed wetlands and natural water bodies, as these organisms remove nutrients and provide large surfaces for biofilms, which are beneficial for nitrogen removal, particularly from submerged macrophyte-dominated water columns. However, information on the responses of biofilms to submerged macrophytes and nitrogen molecules is limited. In the present study, bacterial community structure and denitrifiers were investigated in biofilms on the leaves of four submerged macrophytes and artificial plants exposed to two nitrate concentrations. The biofilm cells were evenly distributed on artificial plants but appeared in microcolonies on the surfaces of submerged macrophytes. Proteobacteria was the most abundant phylum in all samples, accounting for 27.3-64.8% of the high-quality bacterial reads, followed by Chloroflexi (3.7-25.4%), Firmicutes (3.0-20.1%), Acidobacteria (2.7-15.7%), Actinobacteria (2.2-8.7%), Bacteroidetes (0.5-9.7%), and Verrucomicrobia (2.4-5.2%). Cluster analysis showed that bacterial community structure can be significantly different on macrophytes versus from those on artificial plants. Redundancy analysis showed that electrical conductivity and nitrate concentration were positively correlated with Shannon index and operational taxonomic unit (OTU) richness (log10 transformed) but somewhat negatively correlated with microbial density. The relative abundances of five denitrifying genes were positively correlated with nitrate concentration and electrical conductivity but negatively correlated with dissolved oxygen.

The isolation and characterization of actinobacteria from dominant benthic macroinvertebrates endemic to Lake Baikal.

PubMed

Axenov-Gribanov, Denis; Rebets, Yuriy; Tokovenko, Bogdan; Voytsekhovskaya, Irina; Timofeyev, Maxim; Luzhetskyy, Andriy

2016-03-01

The high demand for new antibacterials fosters the isolation of new biologically active compounds producing actinobacteria. Here, we report the isolation and initial characterization of cultured actinobacteria from dominant benthic organisms' communities of Lake Baikal. Twenty-five distinct strains were obtained from 5 species of Baikal endemic macroinvertebrates of amphipods, freshwater sponges, turbellaria worms, and insects (caddisfly larvae). The 16S ribosomal RNA (rRNA)-based phylogenic analysis of obtained strains showed their affiliation to Streptomyces, Nocardia, Pseudonocardia, Micromonospora, Aeromicrobium, and Agromyces genera, revealing the diversity of actinobacteria associated with the benthic organisms of Lake Baikal. The biological activity assays showed that 24 out of 25 strains are producing compounds active against at least one of the test cultures used, including Gram-negative bacteria and Candida albicans. Complete dereplication of secondary metabolite profiles of two isolated strains led to identification of only few known compounds, while the majority of detected metabolites are not listed in existing antibiotic databases.

Antibacterial, Anticancer and Neuroprotective Activities of Rare Actinobacteria from Mangrove Forest Soils.

PubMed

Azman, Adzzie-Shazleen; Othman, Iekhsan; Fang, Chee-Mun; Chan, Kok-Gan; Goh, Bey-Hing; Lee, Learn-Han

2017-06-01

Mangrove is a complex ecosystem that contains diverse microbial communities, including rare actinobacteria with great potential to produce bioactive compounds. To date, bioactive compounds extracted from mangrove rare actinobacteria have demonstrated diverse biological activities. The discovery of three novel rare actinobacteria by polyphasic approach, namely Microbacterium mangrovi MUSC 115 T , Sinomonas humi MUSC 117 T and Monashia flava MUSC 78 T from mangrove soils at Tanjung Lumpur, Peninsular Malaysia have led to the screening on antibacterial, anticancer and neuroprotective activities. A total of ten different panels of bacteria such as Methicillin-resistant Staphylococcus aureus (MRSA) ATCC 43300, ATCC 70069, Pseudomonas aeruginosa NRBC 112582 and others were selected for antibacterial screening. Three different neuroprotective models (hypoxia, oxidative stress, dementia) were done using SHSY5Y neuronal cells while two human cancer cells lines, namely human colon cancer cell lines (HT-29) and human cervical carcinoma cell lines (Ca Ski) were utilized for anticancer activity. The result revealed that all extracts exhibited bacteriostatic effects on the bacteria tested. On the other hand, the neuroprotective studies demonstrated M. mangrovi MUSC 115 T extract exhibited significant neuroprotective properties in oxidative stress and dementia model while the extract of strain M. flava MUSC 78 T was able to protect the SHSY5Y neuronal cells in hypoxia model. Furthermore, the extracts of M. mangrovi MUSC 115 T and M. flava MUSC 78 T exhibited anticancer effect against Ca Ski cell line. The chemical analysis of the extracts through GC-MS revealed that the majority of the compounds present in all extracts are heterocyclic organic compound that could explain for the observed bioactivities. Therefore, the results obtained in this study suggested that rare actinobacteria discovered from mangrove environment could be potential sources of antibacterial, anticancer and

[Isolation and physiological characteristics of endophytic actinobacteria from medicinal plants].

PubMed

Du, Huijing; Su, Jing; Yu, Liyan; Zhang, Yuqin

2013-01-04

To isolate, incubate and characterize cultivable endophytic antinobacteria from medicinal plants, and analyze the diversity of the endophytic antinobacteria, then explore the novel microbial resources. Ten media were used to isolate endophytic antinobacteria from 37 fresh medicinal plant tissue samples. The optimal cultivation conditions for endophytic antinobacteria were determined by comparison. Based on the morphology of the colonies and cells of the new isolates, we chose 174 isolates to analyze their 16S rRNA gene sequences and the diversity of the medicinal plant endophytic antinobacteria. The physiological characteristics of 27 representative strains were studied using Biolog GEN III MicroPlates, API 50CH and API ZYM kits. In total 940 endophytics affiliated to 47 genera of 30 families were isolated, among which more than 600 actinobacteria belonged to 34 genera and 7 unknown taxa. Good growth of the endophytic antinobacteria on PYG (peptone-yeast-glycerol) medium with pH 7.2 at 28-32 degrees C was observed. Physiological characteristics differences of these isolates related to their phylogenetic relationships. Greater differences were shown among the strains from the same host plants than those from differ,ent plants grown in the same area. There are great diverse endophytic actinobacteria inside the medicinal plants. No direct relationship of the endophytic actinobacteria from medicinal plants with the host plants in the sole carbon source utilization, fermentation of carbon sources to produce acid and the enzyme activities was found, while it seemed that the physiological characteristics of the isolates related to the geographical distribution of their host.

Antituberculotic activity of actinobacteria isolated from the rare habitats.

PubMed

Hussain, A; Rather, M A; Shah, A M; Bhat, Z S; Shah, A; Ahmad, Z; Parvaiz Hassan, Q

2017-09-01

A distinctive screening procedure resulted in the isolation and identification of antituberculotic actinobacteria. In this course, a total of 125 actinobacteria were isolated from various soil samples from untapped areas in Northwestern Himalayas, India. The antibacterial screening showed that 26 isolates inhibited the growth of at least one of the tested bacterial pathogens including Staphylococcus aureus (ATCC 25923), Staphylococcus epidermidis (ATCC 12228), Bacillus subtilis (ATCC 11774), Micrococcus luteus (ATCC 10240), Escherichia coli (10536), Pseudomonas aeruginosa (ATCC 10145) and Klebsiella pneumonia (ATCC BAA-2146). The production media was optimized for the active strains by estimation of their extract value by the quantification of the ethyl acetate extract. The screening of fermentation products from the selected 26 bioactive isolates revealed that 10 strains have metabolites antagonistic against the standard H37Rv strain of Mycobacterium tuberculosis. The characterization by 16S rRNA gene sequencing and phylogenetic analysis demonstrated the diverse nature of these antituberculosis strains. The secondary metabolites of potent, rare strain, Lentzea violacea AS08 exhibited promising antituberculosis activity with minimal inhibitory concentration (MIC) of 3·9 μg ml -1 . The metabolites identified by gas chromatography-mass spectrometry (GC-MS) included, Phenol, 2,5-bis (1, 1-dimethylethyl), n-Hexadecanoic acid, Hexadecanoic acid methyl-ester, Hexadecanoic acid ethyl-ester and, 9,12-Octadecadienoyl chloride(Z,Z) are biologically significant molecules. The study presents the isolation of rare actinobacteria from untapped sites in the Northwestern Himalayas and their in vitro potential against Mycobacterium tuberculosis for their metabolites. The study revealed that exploring the untapped natural sources as one of the resourceful approaches for the discovery of new natural products. This study also provided strong evidence for the ability of rare and

Comparative analysis of the gastrointestinal microbial communities of bar-headed goose (Anser indicus) in different breeding patterns by high-throughput sequencing.

PubMed

Wang, Wen; Cao, Jian; Li, Ji-Rong; Yang, Fang; Li, Zhuo; Li, Lai-Xing

2016-01-01

The bar-headed goose is currently one of the most popular species for rare birds breeding in China. However, bar-headed geese in captivity display a reduced reproductive rate. The gut microbiome has been shown to influence host factors such as nutrient and energy metabolism, immune homeostasis and reproduction. It is therefore of great scientific and agriculture value to analyze the microbial communities associated with bar-headed geese in order to improve their reproductive rate. Here we describe the first comparative study of the gut microbial communities of bar-headed geese in three different breeding pattern groups by 16SrRNA sequences using the Illumina MiSeq platform. The results showed that Firmicutes predominated (58.33%) among wild bar-headed geese followed by Proteobacteria (30.67%), Actinobacteria (7.33%) and Bacteroidetes (3.33%). In semi-artificial breeding group, Firmicutes was also the most abundant bacteria (62.00%), followed by Bacteroidetes (28.67%), Proteobacteria (4.20%), Actinobacteria (3.27%) and Fusobacteria (1.51%). The microbial communities of artificial breeding group were dominated by Firmicutes (60.67%), Fusobacteria (29.67%) and Proteobacteria (9.33%). Wild bar-headed geese had a significant higher relative abundance of Proteobacteria and Actinobacteria, while semi-artificial breeding bar-headed geese had significantly more Bacteroidetes. The semi-artificial breeding group had the highest microbial community diversity and richness, followed by wild group, and then the artificial breeding group. The marked differences of genus level group-specific microbes create a baseline for future bar-headed goose microbiology research. Copyright © 2015 Elsevier GmbH. All rights reserved.

Nitrogen deposition and management practices increase soil microbial biomass carbon but decrease diversity in Moso bamboo plantations

PubMed Central

Li, Quan; Song, Xinzhang; Gu, Honghao; Gao, Fei

2016-01-01

Because microbial communities play a key role in carbon (C) and nitrogen (N) cycling, changes in the soil microbial community may directly affect ecosystem functioning. However, the effects of N deposition and management practices on soil microbes are still poorly understood. We studied the effects of these two factors on soil microbial biomass carbon (MBC) and community composition in Moso bamboo plantations using high-throughput sequencing of the 16S rRNA gene. Plantations under conventional (CM) or intensive management (IM) were subjected to one of four N treatments for 30 months. IM and N addition, both separately and in combination, significantly increased soil MBC while decreasing bacterial diversity. However, increases in soil MBC were inhibited when N addition exceeded 60 kg N∙ha−1∙yr−1. IM increased the relative abundances of Actinobacteria and Crenarchaeota but decreased that of Acidobacteria. N addition increased the relative abundances of Acidobacteria, Crenarchaeota, and Actinobacteria but decreased that of Proteobacteria. Soil bacterial diversity was significantly related to soil pH, C/N ratio, and nitrogen and available phosphorus content. Management practices exerted a greater influence over regulation of the soil MBC and microbial diversity compared to that of N deposition in Moso bamboo plantations. PMID:27302857

Nitrogen deposition and management practices increase soil microbial biomass carbon but decrease diversity in Moso bamboo plantations

NASA Astrophysics Data System (ADS)

Li, Quan; Song, Xinzhang; Gu, Honghao; Gao, Fei

2016-06-01

Because microbial communities play a key role in carbon (C) and nitrogen (N) cycling, changes in the soil microbial community may directly affect ecosystem functioning. However, the effects of N deposition and management practices on soil microbes are still poorly understood. We studied the effects of these two factors on soil microbial biomass carbon (MBC) and community composition in Moso bamboo plantations using high-throughput sequencing of the 16S rRNA gene. Plantations under conventional (CM) or intensive management (IM) were subjected to one of four N treatments for 30 months. IM and N addition, both separately and in combination, significantly increased soil MBC while decreasing bacterial diversity. However, increases in soil MBC were inhibited when N addition exceeded 60 kg N•ha-1•yr-1. IM increased the relative abundances of Actinobacteria and Crenarchaeota but decreased that of Acidobacteria. N addition increased the relative abundances of Acidobacteria, Crenarchaeota, and Actinobacteria but decreased that of Proteobacteria. Soil bacterial diversity was significantly related to soil pH, C/N ratio, and nitrogen and available phosphorus content. Management practices exerted a greater influence over regulation of the soil MBC and microbial diversity compared to that of N deposition in Moso bamboo plantations.

Responsiveness of soil nitrogen fractions and bacterial communities to afforestation in the Loess Hilly Region (LHR) of China

NASA Astrophysics Data System (ADS)

Ren, Chengjie; Sun, Pingsheng; Kang, Di; Zhao, Fazhu; Feng, Yongzhong; Ren, Guangxin; Han, Xinhui; Yang, Gaihe

2016-06-01

In the present paper, we investigated the effects of afforestation on nitrogen fractions and microbial communities. A total of 24 soil samples were collected from farmland (FL) and three afforested lands, namely Robinia pseudoacacia L (RP), Caragana korshinskii Kom (CK), and abandoned land (AL), which have been arable for the past 40 years. Quantitative PCR and Illumina sequencing of 16S rRNA genes were used to analyze soil bacterial abundance, diversity, and composition. Additionally, soil nitrogen (N) stocks and fractions were estimated. The results showed that soil N stock, N fractions, and bacterial abundance and diversity increased following afforestation. Proteobacteria, Acidobacteria, and Actinobacteria were the dominant phyla of soil bacterial compositions. Overall, soil bacterial compositions generally changed from Actinobacteria (Acidobacteria)-dominant to Proteobacteria-dominant following afforestation. Soil N fractions, especially for dissolved organic nitrogen (DON), were significantly correlated with most bacterial groups and bacterial diversity, while potential competitive interactions between Proteobacteria (order Rhizobiales) and Cyanobacteria were suggested. In contrast, nitrate nitrogen (NO3--N) influenced soil bacterial compositions less than other N fractions. Therefore, the present study demonstrated that bacterial diversity and specific species respond to farmland-to-forest conversion and hence have the potential to affect N dynamic processes in the Loess Plateau.

Complete Genome Sequence of a New Firmicutes Species Isolated from Anaerobic Biomass Hydrolysis.

PubMed

Abendroth, Christian; Hahnke, Sarah; Codoñer, Francisco M; Klocke, Michael; Luschnig, Olaf; Porcar, Manuel

2017-10-05

A new Firmicutes isolate, strain HV4-6-A5C, was obtained from the hydrolysis stage of a mesophilic and anaerobic two-stage lab-scale leach-bed system for biomethanation of fresh grass. It is assumed that the bacterial isolate contributes to plant biomass degradation. Here, we report a draft annotated genome sequence of this organism. Copyright © 2017 Abendroth et al.

Phylogenetic relatedness determined between antibiotic resistance and 16S rRNA genes in actinobacteria.

PubMed

Sagova-Mareckova, Marketa; Ulanova, Dana; Sanderova, Petra; Omelka, Marek; Kamenik, Zdenek; Olsovska, Jana; Kopecky, Jan

2015-04-01

Distribution and evolutionary history of resistance genes in environmental actinobacteria provide information on intensity of antibiosis and evolution of specific secondary metabolic pathways at a given site. To this day, actinobacteria producing biologically active compounds were isolated mostly from soil but only a limited range of soil environments were commonly sampled. Consequently, soil remains an unexplored environment in search for novel producers and related evolutionary questions. Ninety actinobacteria strains isolated at contrasting soil sites were characterized phylogenetically by 16S rRNA gene, for presence of erm and ABC transporter resistance genes and antibiotic production. An analogous analysis was performed in silico with 246 and 31 strains from Integrated Microbial Genomes (JGI_IMG) database selected by the presence of ABC transporter genes and erm genes, respectively. In the isolates, distances of erm gene sequences were significantly correlated to phylogenetic distances based on 16S rRNA genes, while ABC transporter gene distances were not. The phylogenetic distance of isolates was significantly correlated to soil pH and organic matter content of isolation sites. In the analysis of JGI_IMG datasets the correlation between phylogeny of resistance genes and the strain phylogeny based on 16S rRNA genes or five housekeeping genes was observed for both the erm genes and ABC transporter genes in both actinobacteria and streptomycetes. However, in the analysis of sequences from genomes where both resistance genes occurred together the correlation was observed for both ABC transporter and erm genes in actinobacteria but in streptomycetes only in the erm gene. The type of erm resistance gene sequences was influenced by linkage to 16S rRNA gene sequences and site characteristics. The phylogeny of ABC transporter gene was correlated to 16S rRNA genes mainly above the genus level. The results support the concept of new specific secondary metabolite

Characterizing bacterial communities in tilapia pond surface sediment and their responses to pond differences and temporal variations.

PubMed

Fan, Limin; Barry, Kamira; Hu, Gengdong; Meng, Shunlong; Song, Chao; Qiu, Liping; Zheng, Yao; Wu, Wei; Qu, Jianhong; Chen, Jiazhang; Xu, Pao

2017-01-01

Bacterial community compositions in the surface sediment of tilapia ponds and their responses to pond characteristics or seasonal variations were investigated. For that, three ponds with different stocking densities were selected to collect the samples. And the method of Illumina high-throughput sequencing was used to amplify the bacterial 16S rRNA genes. A total of 662, 876 valid reads and 5649 operational taxonomic units were obtained. Further analysis showed that the dominant phyla in all three ponds were Proteobacteria, Bacteroidetes, Chloroflexi, and Acidobacteria. The phyla Planctomycetes, Firmicutes, Chlorobi, and Spirochaetae were also relatively abundant. Among the eight phyla, the abundances of only Proteobacteria, Bacteroidetes, Firmicutes, and Spirochaetae were affected by seasonal variations, while seven of these (with the exception of Acidobacteria) were affected by pond differences. A comprehensive analysis of the richness and diversity of the bacterial 16S rRNA gene, and of the similarity in bacterial community composition in sediment also showed that the communities in tilapia pond sediment were shaped more by pond differences than by seasonal variations. Linear discriminant analysis further indicated that the influences of pond characteristics on sediment bacterial communities might be related to feed coefficients and stocking densities of genetically improved farmed tilapia (GIFT).

Isolation, diversity, and antimicrobial activity of rare actinobacteria from medicinal plants of tropical rain forests in Xishuangbanna, China.

PubMed

Qin, Sheng; Li, Jie; Chen, Hua-Hong; Zhao, Guo-Zhen; Zhu, Wen-Yong; Jiang, Cheng-Lin; Xu, Li-Hua; Li, Wen-Jun

2009-10-01

Endophytic actinobacteria are relatively unexplored as potential sources of novel species and novel natural products for medical and commercial exploitation. Xishuangbanna is recognized throughout the world for its diverse flora, especially the rain forest plants, many of which have indigenous pharmaceutical histories. However, little is known about the endophytic actinobacteria of this tropical area. In this work, we studied the diversity of actinobacteria isolated from medicinal plants collected from tropical rain forests in Xishuangbanna. By the use of different selective isolation media and methods, a total of 2,174 actinobacteria were isolated. Forty-six isolates were selected on the basis of their morphologies on different media and were further characterized by 16S rRNA gene sequencing. The results showed an unexpected level of diversity, with 32 different genera. To our knowledge, this is the first report describing the isolation of Saccharopolyspora, Dietzia, Blastococcus, Dactylosporangium, Promicromonospora, Oerskovia, Actinocorallia, and Jiangella species from endophytic environments. At least 19 isolates are considered novel taxa by our current research. In addition, all 46 isolates were tested for antimicrobial activity and were screened for the presence of genes encoding polyketide synthetases and nonribosomal peptide synthetases. The results confirm that the medicinal plants of Xishuangbanna represent an extremely rich reservoir for the isolation of a significant diversity of actinobacteria, including novel species, that are potential sources for the discovery of biologically active compounds.

Diversity and antibacterial activity of culturable actinobacteria isolated from five species of the South China Sea gorgonian corals.

PubMed

Zhang, Xiao-Yong; He, Fei; Wang, Guang-Hua; Bao, Jie; Xu, Xin-Ya; Qi, Shu-Hua

2013-06-01

This study describes the diversity and antibacterial activity of culturable actinobacteria isolated from five species of gorgonian corals (Echinogorgia aurantiaca, Melitodes squamata, Muricella flexuosa, Subergorgia suberosa, and Verrucella umbraculum) collected in shallow water of the South China Sea. A total of 123 actinobacterial isolates were recovered using ten different isolation media, and assigned to 11 genera, including Streptomyces and Micromonospora as the dominant genera, followed by Nocardia, Verrucosispora, Nocardiopsis, Rhodococcus, Pseudonocardia, Agrococcus, Saccharomonospora, Saccharopolyspora and Dietzia. Comparable analysis indicated that the numbers of actinobacterial genera and isolates from the five gorgonian coral species varied significantly. It was found that 72 isolates displayed antibacterial activity against at least one indicator bacterium, and the antibacterial strains isolated from different gorgonians had almost the same proportion (~50 %). These results provide direct evidence for the hypotheses that gorgonian coral species contain large and diverse communities of actinobacteria, and suggest that many gorgonian-associated actinobacteria could produce some antibacterial agents to protect their hosts against pathogens. To our knowledge, this is the first report about the diversity of culturable actinobacteria isolated from gorgonian corals.

Exploring the Diversity and Antimicrobial Potential of Marine Actinobacteria from the Comau Fjord in Northern Patagonia, Chile

PubMed Central

Undabarrena, Agustina; Beltrametti, Fabrizio; Claverías, Fernanda P.; González, Myriam; Moore, Edward R. B.; Seeger, Michael; Cámara, Beatriz

2016-01-01

Bioprospecting natural products in marine bacteria from fjord environments are attractive due to their unique geographical features. Although, Actinobacteria are well known for producing a myriad of bioactive compounds, investigations regarding fjord-derived marine Actinobacteria are scarce. In this study, the diversity and biotechnological potential of Actinobacteria isolated from marine sediments within the Comau fjord, in Northern Chilean Patagonia, were assessed by culture-based approaches. The 16S rRNA gene sequences revealed that members phylogenetically related to the Micrococcaceae, Dermabacteraceae, Brevibacteriaceae, Corynebacteriaceae, Microbacteriaceae, Dietziaceae, Nocardiaceae, and Streptomycetaceae families were present at the Comau fjord. A high diversity of cultivable Actinobacteria (10 genera) was retrieved by using only five different isolation media. Four isolates belonging to Arthrobacter, Brevibacterium, Corynebacterium and Kocuria genera showed 16S rRNA gene identity <98.7% suggesting that they are novel species. Physiological features such as salt tolerance, artificial sea water requirement, growth temperature, pigmentation and antimicrobial activity were evaluated. Arthrobacter, Brachybacterium, Curtobacterium, Rhodococcus, and Streptomyces isolates showed strong inhibition against both Gram-negative Pseudomonas aeruginosa, Escherichia coli and Salmonella enterica and Gram-positive Staphylococcus aureus, Listeria monocytogenes. Antimicrobial activities in Brachybacterium, Curtobacterium, and Rhodococcus have been scarcely reported, suggesting that non-mycelial strains are a suitable source of bioactive compounds. In addition, all strains bear at least one of the biosynthetic genes coding for NRPS (91%), PKS I (18%), and PKS II (73%). Our results indicate that the Comau fjord is a promising source of novel Actinobacteria with biotechnological potential for producing biologically active compounds. PMID:27486455

A proteomic survey of nonribosomal peptide and polyketide biosynthesis in actinobacteria

USDA-ARS?s Scientific Manuscript database

Actinobacteria such as streptomycetes are renowned for their ability to produce bioactive natural products including nonribosomal peptides (NRPs) and polyketides (PKs). The advent of genome sequencing has revealed an even larger genetic repertoire for secondary metabolism with most of the small mole...

A primary assessment of the endophytic bacterial community in a xerophilous moss (Grimmia montana) using molecular method and cultivated isolates

PubMed Central

Liu, Xiao Lei; Liu, Su Lin; Liu, Min; Kong, Bi He; Liu, Lei; Li, Yan Hong

2014-01-01

Investigating the endophytic bacterial community in special moss species is fundamental to understanding the microbial-plant interactions and discovering the bacteria with stresses tolerance. Thus, the community structure of endophytic bacteria in the xerophilous moss Grimmia montana were estimated using a 16S rDNA library and traditional cultivation methods. In total, 212 sequences derived from the 16S rDNA library were used to assess the bacterial diversity. Sequence alignment showed that the endophytes were assigned to 54 genera in 4 phyla (Proteobacteria, Firmicutes, Actinobacteria and Cytophaga/Flexibacter/Bacteroids). Of them, the dominant phyla were Proteobacteria (45.9%) and Firmicutes (27.6%), the most abundant genera included Acinetobacter, Aeromonas, Enterobacter, Leclercia, Microvirga, Pseudomonas, Rhizobium, Planococcus, Paenisporosarcina and Planomicrobium. In addition, a total of 14 species belonging to 8 genera in 3 phyla (Proteobacteria, Firmicutes, Actinobacteria) were isolated, Curtobacterium, Massilia, Pseudomonas and Sphingomonas were the dominant genera. Although some of the genera isolated were inconsistent with those detected by molecular method, both of two methods proved that many different endophytic bacteria coexist in G. montana. According to the potential functional analyses of these bacteria, some species are known to have possible beneficial effects on hosts, but whether this is the case in G. montana needs to be confirmed. PMID:24948927

Diversity and Antimicrobial Activities of Actinobacteria Isolated from Tropical Mangrove Sediments in Malaysia

PubMed Central

Lee, Learn-Han; Zainal, Nurullhudda; Azman, Adzzie-Shazleen; Eng, Shu-Kee; Goh, Bey-Hing; Yin, Wai-Fong; Ab Mutalib, Nurul-Syakima; Chan, Kok-Gan

2014-01-01

The aim of this study was to isolate and identify Actinobacteria from Malaysia mangrove forest and screen them for production of antimicrobial secondary metabolites. Eighty-seven isolates were isolated from soil samples collected at 4 different sites. This is the first report to describe the isolation of Streptomyces, Mycobacterium, Leifsonia, Microbacterium, Sinomonas, Nocardia, Terrabacter, Streptacidiphilus, Micromonospora, Gordonia, and Nocardioides from mangrove in east coast of Malaysia. Of 87 isolates, at least 5 isolates are considered as putative novel taxa. Nine Streptomyces sp. isolates were producing potent antimicrobial secondary metabolites, indicating that Streptomyces isolates are providing high quality metabolites for drug discovery purposes. The discovery of a novel species, Streptomyces pluripotens sp. nov. MUSC 135T that produced potent secondary metabolites inhibiting the growth of MRSA, had provided promising metabolites for drug discovery research. The biosynthetic potential of 87 isolates was investigated by the detection of polyketide synthetase (PKS) and nonribosomal polyketide synthetase (NRPS) genes, the hallmarks of secondary metabolites production. Results showed that many isolates were positive for PKS-I (19.5%), PKS-II (42.5%), and NRPS (5.7%) genes, indicating that mangrove Actinobacteria have significant biosynthetic potential. Our results highlighted that mangrove environment represented a rich reservoir for isolation of Actinobacteria, which are potential sources for discovery of antimicrobial secondary metabolites. PMID:25162061

Diversity and antimicrobial activities of actinobacteria isolated from tropical mangrove sediments in Malaysia.

PubMed

Lee, Learn-Han; Zainal, Nurullhudda; Azman, Adzzie-Shazleen; Eng, Shu-Kee; Goh, Bey-Hing; Yin, Wai-Fong; Ab Mutalib, Nurul-Syakima; Chan, Kok-Gan

2014-01-01

The aim of this study was to isolate and identify Actinobacteria from Malaysia mangrove forest and screen them for production of antimicrobial secondary metabolites. Eighty-seven isolates were isolated from soil samples collected at 4 different sites. This is the first report to describe the isolation of Streptomyces, Mycobacterium, Leifsonia, Microbacterium, Sinomonas, Nocardia, Terrabacter, Streptacidiphilus, Micromonospora, Gordonia, and Nocardioides from mangrove in east coast of Malaysia. Of 87 isolates, at least 5 isolates are considered as putative novel taxa. Nine Streptomyces sp. isolates were producing potent antimicrobial secondary metabolites, indicating that Streptomyces isolates are providing high quality metabolites for drug discovery purposes. The discovery of a novel species, Streptomyces pluripotens sp. nov. MUSC 135(T) that produced potent secondary metabolites inhibiting the growth of MRSA, had provided promising metabolites for drug discovery research. The biosynthetic potential of 87 isolates was investigated by the detection of polyketide synthetase (PKS) and nonribosomal polyketide synthetase (NRPS) genes, the hallmarks of secondary metabolites production. Results showed that many isolates were positive for PKS-I (19.5%), PKS-II (42.5%), and NRPS (5.7%) genes, indicating that mangrove Actinobacteria have significant biosynthetic potential. Our results highlighted that mangrove environment represented a rich reservoir for isolation of Actinobacteria, which are potential sources for discovery of antimicrobial secondary metabolites.

Isolation, Diversity, and Antimicrobial Activity of Rare Actinobacteria from Medicinal Plants of Tropical Rain Forests in Xishuangbanna, China▿ †

PubMed Central

Qin, Sheng; Li, Jie; Chen, Hua-Hong; Zhao, Guo-Zhen; Zhu, Wen-Yong; Jiang, Cheng-Lin; Xu, Li-Hua; Li, Wen-Jun

2009-01-01

Endophytic actinobacteria are relatively unexplored as potential sources of novel species and novel natural products for medical and commercial exploitation. Xishuangbanna is recognized throughout the world for its diverse flora, especially the rain forest plants, many of which have indigenous pharmaceutical histories. However, little is known about the endophytic actinobacteria of this tropical area. In this work, we studied the diversity of actinobacteria isolated from medicinal plants collected from tropical rain forests in Xishuangbanna. By the use of different selective isolation media and methods, a total of 2,174 actinobacteria were isolated. Forty-six isolates were selected on the basis of their morphologies on different media and were further characterized by 16S rRNA gene sequencing. The results showed an unexpected level of diversity, with 32 different genera. To our knowledge, this is the first report describing the isolation of Saccharopolyspora, Dietzia, Blastococcus, Dactylosporangium, Promicromonospora, Oerskovia, Actinocorallia, and Jiangella species from endophytic environments. At least 19 isolates are considered novel taxa by our current research. In addition, all 46 isolates were tested for antimicrobial activity and were screened for the presence of genes encoding polyketide synthetases and nonribosomal peptide synthetases. The results confirm that the medicinal plants of Xishuangbanna represent an extremely rich reservoir for the isolation of a significant diversity of actinobacteria, including novel species, that are potential sources for the discovery of biologically active compounds. PMID:19648362

Antimicrobial activity of actinobacteria isolated from the guts of subterranean termites

Treesearch

Rachel Arango; C. M. Carlson; C. R. Currie; B. R. McDonald; A. J. Book; Frederick Green; K. F. Raffa; N.K. Lebow

2016-01-01

Subterranean termites need to minimize potentially pathogenic and competitive fungi in their environment in order to maintain colony health. We examined the ability of Actinobacteria isolated from termite guts in suppressing microorganisms commonly encountered in a subterranean environment. Guts from two subterranean termite species, Reticulitermes flavipes...

Microbial Community Structures and Dynamics in the O3/BAC Drinking Water Treatment Process

PubMed Central

Tian, Jian; Lu, Jun; Zhang, Yu; Li, Jian-Cheng; Sun, Li-Chen; Hu, Zhang-Li

2014-01-01

Effectiveness of drinking water treatment, in particular pathogen control during the water treatment process, is always a major public health concern. In this investigation, the application of PCR-DGGE technology to the analysis of microbial community structures and dynamics in the drinking water treatment process revealed several dominant microbial populations including: α-Proteobacteria, β-Proteobacteria, γ-Proteobacteria, Bacteroidetes, Actinobacteria Firmicutes and Cyanobacteria. α-Proteobacteria and β-Proteobacteria were the dominant bacteria during the whole process. Bacteroidetes and Firmicutes were the dominant bacteria before and after treatment, respectively. Firmicutes showed season-dependent changes in population dynamics. Importantly, γ-Proteobacteria, which is a class of medically important bacteria, was well controlled by the O3/biological activated carbon (BAC) treatment, resulting in improved effluent water bio-safety. PMID:24937529

Genomes of Planktonic Acidimicrobiales: Widening Horizons for Marine Actinobacteria by Metagenomics

PubMed Central

Mizuno, Carolina Megumi; Ghai, Rohit

2015-01-01

ABSTRACT The genomes of four novel marine Actinobacteria have been assembled from large metagenomic data sets derived from the Mediterranean deep chlorophyll maximum (DCM). These are the first marine representatives belonging to the order Acidimicrobiales and only the second group of planktonic marine Actinobacteria to be described. Their streamlined genomes and photoheterotrophic lifestyle suggest that they are planktonic, free-living microbes. A novel rhodopsin clade, acidirhodopsins, related to freshwater actinorhodopsins, was found in these organisms. Their genomes suggest a capacity to assimilate C2 compounds, some using the glyoxylate bypass and others with the ethylmalonyl-coenzyme A (CoA) pathway. They are also able to derive energy from dimethylsulfopropionate (DMSP), sulfonate, and carbon monoxide oxidation, all commonly available in the marine habitat. These organisms appear to be prevalent in the deep photic zone at or around the DCM. The presence of sister clades to the marine Acidimicrobiales in freshwater aquatic habitats provides a new example of marine-freshwater transitions with potential evolutionary insights. PMID:25670777

Inter- and intracellular colonization of Arabidopsis roots by endophytic actinobacteria and the impact of plant hormones on their antimicrobial activity.

PubMed

van der Meij, Anne; Willemse, Joost; Schneijderberg, Martinus A; Geurts, René; Raaijmakers, Jos M; van Wezel, Gilles P

2018-05-01

Many actinobacteria live in close association with eukaryotes such as fungi, insects, animals and plants. Plant-associated actinobacteria display (endo)symbiotic, saprophytic or pathogenic life styles, and can make up a substantial part of the endophytic community. Here, we characterised endophytic actinobacteria isolated from root tissue of Arabidopsis thaliana (Arabidopsis) plants grown in soil from a natural ecosystem. Many of these actinobacteria belong to the family of Streptomycetaceae with Streptomyces olivochromogenes and Streptomyces clavifer as well represented species. When seeds of Arabidopsis were inoculated with spores of Streptomyces strain coa1, which shows high similarity to S. olivochromogenes, roots were colonised intercellularly and, unexpectedly, also intracellularly. Subsequent exposure of endophytic isolates to plant hormones typically found in root and shoot tissues of Arabidopsis led to altered antibiotic production against Escherichia coli and Bacillus subtilis. Taken together, our work reveals remarkable colonization patterns of endophytic streptomycetes with specific traits that may allow a competitive advantage inside root tissue.

The diversity and biogeography of the communities of Actinobacteria in the forelands of glaciers at a continental scale

NASA Astrophysics Data System (ADS)

Zhang, Binglin; Wu, Xiukun; Zhang, Gaosen; Li, Shuyan; Zhang, Wei; Chen, Ximing; Sun, Likun; Zhang, Baogui; Liu, Guangxiu; Chen, Tuo

2016-05-01

Glacier forelands, where the initially exposed area is unvegetated with minimal human influence, are an ideal place for research on the distributions and biogeography of microbial communities. Actinobacteria produce many bioactive substances and have important roles in soil development and biogeochemical cycling. However, little is known about the distribution and biogeography of Actinobacteria in glacier forelands. Therefore, we investigated the patterns of diversity and the biogeography of actinobacterial communities of the inhabited forefields of 5 glaciers in China. Of the bacteria, the mean relative abundance of Actinobacteria was 13.1%, and 6 classes were identified in the phylum Actinobacteria. The dominant class was Actinobacteria (57%), which was followed in abundance by Acidimicrobiia (19%) and Thermoleophilia (19%). When combined, the relative abundance of the other three classes, the MB-A2-108, Nitriliruptoria and Rubrobacteria, was only 2.4%. A biogeographic pattern in the forelands of the 5 glaciers in China was not detected for actinobacterial communities. Compared with 7 other actinobacterial communities found in the forelands of glaciers globally, those in the Southern Hemisphere were significantly different from those in the Northern Hemisphere. Moreover, the communities were significantly different on the separate continents of the Northern Hemisphere. The dissimilarity of the actinobacterial communities increased with geographic distance (r = 0.428, p = 0.0003). Because of environmental factors, the effect of geography was clear when the distance exceeded a certain continent-level threshold. With the analysis of indicator species, we found that each genus had a geographic characteristic, which could explain why the communities with greater diversity were more strongly affected by biogeography.

Environmental Controls Over Actinobacteria Communities in Ecological Sensitive Yanshan Mountains Zone

PubMed Central

Tang, Hui; Shi, Xunxun; Wang, Xiaofei; Hao, Huanhuan; Zhang, Xiu-Min; Zhang, Li-Ping

2016-01-01

The Yanshan Mountains are one of the oldest mountain ranges in the world. They are located in an ecologically sensitive zone in northern China near the Hu Huanyong Line. In this metagenomic study, we investigated the diversity of Actinobacteria in soils at 10 sites (YS1–YS10) on the Yanshan Mountains. First, we assessed the effect of different soil prtreatment on Actinobacteria recovery. With the soil pretreatment method: air drying of the soil sample, followed by exposure to 120°C for 1 h, we observed the higher Actinobacteria diversity in a relatively small number of clone libraries. No significant differences were observed in the Actinobacterial diversity of soils from sites YS2, YS3, YS4, YS6, YS8, YS9, or YS10 (P > 0.1). However, there were differences (P < 0.05) from the YS7 site and other sites, especially in response to environmental change. And we observed highly significant differences (P < 0.001) in Actinobacterial diversity of the soil from YS7 and that from YS4 and YS8 sites. The climatic characteristics of mean active accumulated temperature, annual mean precipitation, and annual mean temperature, and biogeochemical data of total phosphorus contributed to the diversity of Actinobacterial communities in soils at YS1, YS3, YS4, and YS5 sites. Compared to the climatic factors, the biogeochemical factors mostly contributed in shaping the Actinobacterial community. This work provides evidence that the diversity of Actinobacterial communities in soils from the Yashan Mountains show regional biogeographic patterns and that community membership change along the north-south distribution of the Hu Huanyong Line. PMID:27047461

Enhancing the Thermal Resistance of a Novel Acidobacteria-Derived Phytase by Engineering of Disulfide Bridges.

PubMed

Tan, Hao; Miao, Renyun; Liu, Tianhai; Cao, Xuelian; Wu, Xiang; Xie, Liyuan; Huang, Zhongqian; Peng, Weihong; Gan, Bingcheng

2016-10-28

A novel phytase of Acidobacteria was identified from a soil metagenome, cloned, overexpressed, and purified. It has low sequence similarity (<44%) to all the known phytases. At the optimum pH (2.5), the phytase shows an activity level of 1,792 μmol/min/mg at physiological temperature (37°C) and could retain 92% residual activity after 30 min, indicating the phytase is acidophilic and acidostable. However the phytase shows poor stability at high temperatures. To improve its thermal resistance, the enzyme was redesigned using Disulfide by Design 2.0, introducing four additional disulfide bridges. The half-life time of the engineered phytase at 60°C and 80°C, respectively, is 3.0× and 2.8× longer than the wild-type, and its activity and acidostability are not significantly affected.

Codon usage bias in phylum Actinobacteria: relevance to environmental adaptation and host pathogenicity.

PubMed

Lal, Devi; Verma, Mansi; Behura, Susanta K; Lal, Rup

2016-10-01

Actinobacteria are Gram-positive bacteria commonly found in soil, freshwater and marine ecosystems. In this investigation, bias in codon usages of ninety actinobacterial genomes was analyzed by estimating different indices of codon bias such as Nc (effective number of codons), SCUO (synonymous codon usage order), RSCU (relative synonymous codon usage), as well as sequence patterns of codon contexts. The results revealed several characteristic features of codon usage in Actinobacteria, as follows: 1) C- or G-ending codons are used frequently in comparison with A- and U ending codons; 2) there is a direct relationship of GC content with use of specific amino acids such as alanine, proline and glycine; 3) there is an inverse relationship between GC content and Nc estimates, 4) there is low SCUO value (<0.5) for most genes; and 5) GCC-GCC, GCC-GGC, GCC-GAG and CUC-GAC are the frequent context sequences among codons. This study highlights the fact that: 1) in Actinobacteria, extreme GC content and codon bias are driven by mutation rather than natural selection; (2) traits like aerobicity are associated with effective natural selection and therefore low GC content and low codon bias, demonstrating the role of both mutational bias and translational selection in shaping the habitat and phenotype of actinobacterial species. Copyright © 2016 Institut Pasteur. Published by Elsevier Masson SAS. All rights reserved.

Antimicrobial potential of actinobacteria isolated from the rhizosphere of the Caatinga biome plant Caesalpinia pyramidalis Tul.

PubMed

Silva-Lacerda, G R; Santana, R C F; Vicalvi-Costa, M C V; Solidônio, E G; Sena, K X F R; Lima, G M S; Araújo, J M

2016-03-04

Actinobacteria are known to produce various secondary metabolites having antibiotic effects. This study assessed the antimicrobial potential of actinobacteria isolated from the rhizosphere of Caesalpinia pyramidalis Tul. from the Caatinga biome. Sixty-eight actinobacteria isolates were evaluated for antimicrobial activity against different microorganisms by disk diffusion and submerged fermentation, using different culture media, followed by determination of minimum inhibitory concentration (MIC) and chemical prospecting of the crude extract. Of the isolates studied, 52.9% of those isolated at 37°C and 47.05% of those isolated at 45°C had activity against Bacillus subtilis, Staphylococcus aureus, methicillin-resistant S. aureus (MRSA), Fusarium moniliforme, and Candida albicans. When compared with others actinobacteria, the isolate C1.129 stood out with better activity and was identified by 16S rDNA gene analysis as Streptomyces parvulus. The crude ethanol extract showed an MIC of 0.97 μg/mL for MRSA and B. subtilis, while the ethyl acetate extract showed MIC of 3.9 μg/mL for S. aureus and MRSA, showing the greatest potential among the metabolites produced. Chemical prospecting revealed the presence of mono/sesquiterpenes, proanthocyanidin, triterpenes, and steroids in both crude extracts. This study evaluates S. parvulus activity against multi-resistant microorganisms such as MRSA. Thus, it proves that low-fertility soil, as is found in the Caatinga, may contain important microorganisms for the development of new antimicrobial drugs.

Structural and Phylogenetic Analysis of a Conserved Actinobacteria-Specific Protein (ASP1; SCO1997) from Streptomyces Coelicolor

DOE Office of Scientific and Technical Information (OSTI.GOV)

Gao, B.; Sugiman-Marangos, S; Junop, M

2009-01-01

The Actinobacteria phylum represents one of the largest and most diverse groups of bacteria, encompassing many important and well-characterized organisms including Streptomyces, Bifidobacterium, Corynebacterium and Mycobacterium. Members of this phylum are remarkably diverse in terms of life cycle, morphology, physiology and ecology. Recent comparative genomic analysis of 19 actinobacterial species determined that only 5 genes of unknown function uniquely define this large phylum [1]. The cellular functions of these actinobacteria-specific proteins (ASP) are not known.

Acidobacteria appear to dominate the microbiome of two sympatric Caribbean Sponges and one Zoanthid.

PubMed

O'Connor-Sánchez, Aileen; Rivera-Domínguez, Adán J; Santos-Briones, César de los; López-Aguiar, Lluvia K; Peña-Ramírez, Yuri J; Prieto-Davo, Alejandra

2014-12-10

Marine invertebrate-associated microbial communities are interesting examples of complex symbiotic systems and are a potential source of biotechnological products. In this work, pyrosequencing-based assessment from bacterial community structures of sediments, two sponges, and one zoanthid collected in the Mexican Caribbean was performed. The results suggest that the bacterial diversity at the species level is higher in the sediments than in the animal samples. Analysis of bacterial communities' structure showed that about two thirds of the bacterial diversity in all the samples belongs to the phyla Acidobacteria and Proteobacteria. The genus Acidobacterium appears to dominate the bacterial community in all the samples, reaching almost 80% in the sponge Hyrtios. Our evidence suggests that the sympatric location of these benthonic species may lead to common bacterial structure features among their bacterial communities. The results may serve as a first insight to formulate hypotheses that lead to more extensive studies of sessile marine organisms' microbiomes from the Mexican Caribbean.

Diversity, Biogeography, and Biodegradation Potential of Actinobacteria in the Deep-Sea Sediments along the Southwest Indian Ridge

PubMed Central

Chen, Ping; Zhang, Limin; Guo, Xiaoxuan; Dai, Xin; Liu, Li; Xi, Lijun; Wang, Jian; Song, Lei; Wang, Yuezhu; Zhu, Yaxin; Huang, Li; Huang, Ying

2016-01-01

The phylum Actinobacteria has been reported to be common or even abundant in deep marine sediments, however, knowledge about the diversity, distribution, and function of actinobacteria is limited. In this study, actinobacterial diversity in the deep sea along the Southwest Indian Ridge (SWIR) was investigated using both 16S rRNA gene pyrosequencing and culture-based methods. The samples were collected at depths of 1662–4000 m below water surface. Actinobacterial sequences represented 1.2–9.1% of all microbial 16S rRNA gene amplicon sequences in each sample. A total of 5 actinobacterial classes, 17 orders, 28 families, and 52 genera were detected by pyrosequencing, dominated by the classes Acidimicrobiia and Actinobacteria. Differences in actinobacterial community compositions were found among the samples. The community structure showed significant correlations to geochemical factors, notably pH, calcium, total organic carbon, total phosphorus, and total nitrogen, rather than to spatial distance at the scale of the investigation. In addition, 176 strains of the Actinobacteria class, belonging to 9 known orders, 18 families, and 29 genera, were isolated. Among these cultivated taxa, 8 orders, 13 families, and 15 genera were also recovered by pyrosequencing. At a 97% 16S rRNA gene sequence similarity, the pyrosequencing data encompassed 77.3% of the isolates but the isolates represented only 10.3% of the actinobacterial reads. Phylogenetic analysis of all the representative actinobacterial sequences and isolates indicated that at least four new orders within the phylum Actinobacteria were detected by pyrosequencing. More than half of the isolates spanning 23 genera and all samples demonstrated activity in the degradation of refractory organics, including polycyclic aromatic hydrocarbons and polysaccharides, suggesting their potential ecological functions and biotechnological applications for carbon recycling. PMID:27621725

Temperature effects on net greenhouse gas production and bacterial communities in arctic thaw ponds.

PubMed

Negandhi, Karita; Laurion, Isabelle; Lovejoy, Connie

2016-08-01

One consequence of High Arctic permafrost thawing is the formation of small ponds, which release greenhouse gases (GHG) from stored carbon through microbial activity. Under a climate with higher summer air temperatures and longer ice-free seasons, sediments of shallow ponds are likely to become warmer, which could influence enzyme kinetics or select for less cryophilic microbes. There is little data on the direct temperature effects on GHG production and consumption or on microbial communities' composition in Arctic ponds. We investigated GHG production over 16 days at 4°C and 9°C in sediments collected from four thaw ponds. Consistent with an enzymatic response, production rates of CO2 and CH4 were significantly greater at higher temperatures, with Q10 varying from 1.2 to 2.5. The bacterial community composition from one pond was followed through the incubation by targeting the V6-V8 variable regions of the 16S rRNA gene and 16S rRNA. Several rare taxa detected from rRNA accounted for significant community compositional changes. At the higher temperature, the relative community contribution from Bacteroidetes decreased by 15% with compensating increases in Betaproteobacteria, Alphaproteobacteria, Firmicutes, Acidobacteria, Verrucomicrobia and Actinobacteria. The increase in experimental GHG production accompanied by changes in community indicates an additional factor to consider in sediment environments when evaluating future climate scenarios. © FEMS 2016. All rights reserved. For permissions, please e-mail: journals.permissions@oup.com.

Gut Bacterial Community of the Xylophagous Cockroaches Cryptocercus punctulatus and Parasphaeria boleiriana

PubMed Central

Berlanga, Mercedes; Llorens, Carlos; Comas, Jaume; Guerrero, Ricardo

2016-01-01

Cryptocercus punctulatus and Parasphaeria boleiriana are two distantly related xylophagous and subsocial cockroaches. Cryptocercus is related to termites. Xylophagous cockroaches and termites are excellent model organisms for studying the symbiotic relationship between the insect and their microbiota. In this study, high-throughput 454 pyrosequencing of 16S rRNA was used to investigate the diversity of metagenomic gut communities of C. punctulatus and P. boleiriana, and thereby to identify possible shifts in symbiont allegiances during cockroaches evolution. Our results revealed that the hindgut prokaryotic communities of both xylophagous cockroaches are dominated by members of four Bacteria phyla: Bacteroidetes, Firmicutes, Proteobacteria, and Actinobacteria. Other identified phyla were Spirochaetes, Planctomycetes, candidatus Saccharibacteria (formerly TM7), and Acidobacteria, each of which represented 1–2% of the total population detected. Community similarity based on phylogenetic relatedness by unweighted UniFrac analyses indicated that the composition of the bacterial community in the two species was significantly different (P < 0.05). Phylogenetic analysis based on the characterized clusters of Bacteroidetes, Spirochaetes, and Deltaproteobacteria showed that many OTUs present in both cockroach species clustered with sequences previously described in termites and other cockroaches, but not with those from other animals or environments. These results suggest that, during their evolution, those cockroaches conserved several bacterial communities from the microbiota of a common ancestor. The ecological stability of those microbial communities may imply the important functional role for the survival of the host of providing nutrients in appropriate quantities and balance. PMID:27054320

[Effect of ground mulch managements on soil bacterial community structure and diversity in the non-irrigated apple orchard in Weibei Loess Plateau].

PubMed

Chen, Yuexing; Wen, Xiaoxia; Sun, Yulin; Zhang, Junli; Lin, Xiaoli; Liao, Yuncheng

2015-07-04

We studied the changes in soil bacterial communities induced by ground mulch managements at different apple growth periods. We adopted the denaturing gradient gel electrophoresis (DGGE) with PCR-amplified 16S rRNA fragments to determine soil bacterial community structure and diversity. Soil bacterial community structure with different ground mulch managements were significantly different. Both the mulch management strategies and apple growth periods affected the predominant groups and their abundance in soil bacterial communities. Grass mulch and cornstalk mulch treatments had higher bacterial diversity and richness than the control at young fruit period and fruit expanding period, whereas film mulch treatment had no significant difference compared with the control. During mature period, bacterial diversity in the control reached its maximum, which may be ascribed to the rapid growth and reproduction of the r-selection bacteria. The clustering and detrended correspondence analysis revealed that differences in soil bacterial communities were closely correlated to apple growth periods and ground mulch managements. Soil samples from the grass mulch and cornstalk mulch treatments clustered together while those mulched with plastic film treatment were similar to the control. The most abundant phylum in soil bacterial community was Proteobacteria followed by Bacteroidetes. Some other phyla were also detected, such as Acidobacteria, Firmicutes, Actinobacteria and Chloroflexi. Mulching with plant (Grass/Cornstalk) had great effects on soil bacterial community structure and enhanced the diversity while film mulch management had no significant effects.

The Structure of Microbial Community and Degradation of Diatoms in the Deep Near-Bottom Layer of Lake Baikal

PubMed Central

Zakharova, Yulia R.; Galachyants, Yuri P.; Kurilkina, Maria I.; Likhoshvay, Alexander V.; Petrova, Darya P.; Shishlyannikov, Sergey M.; Ravin, Nikolai V.; Mardanov, Andrey V.; Beletsky, Alexey V.; Likhoshway, Yelena V.

2013-01-01

Insight into the role of bacteria in degradation of diatoms is important for understanding the factors and components of silica turnover in aquatic ecosystems. Using microscopic methods, it has been shown that the degree of diatom preservation and the numbers of diatom-associated bacteria in the surface layer of bottom sediments decrease with depth; in the near-bottom water layer, the majority of bacteria are associated with diatom cells, being located either on the cell surface or within the cell. The structure of microbial community in the near-bottom water layer has been characterized by pyrosequencing of the 16S rRNA gene, which has revealed 149 208 unique sequences. According to the results of metagenomic analysis, the community is dominated by representatives of Proteobacteria (41.9%), Actinobacteria (16%); then follow Acidobacteria (6.9%), Cyanobacteria (5%), Bacteroidetes (4.7%), Firmicutes (2.8%), Nitrospira (1.6%), and Verrucomicrobia (1%); other phylotypes account for less than 1% each. For 18.7% of the sequences, taxonomic identification has been possible only to the Bacteria domain level. Many bacteria identified to the genus level have close relatives occurring in other aquatic ecosystems and soils. The metagenome of the bacterial community from the near-bottom water layer also contains 16S rRNA gene sequences found in previously isolated bacterial strains possessing hydrolytic enzyme activity. These data show that potential degraders of diatoms occur among the vast variety of microorganisms in the near-bottom water of Lake Baikal. PMID:23560063

Detection of microbial communities in continuous and discontinuous membrane bioreactor using high-density oligonucleotide Microarray

NASA Astrophysics Data System (ADS)

Duan, Liang; Song, Yonghui; Xia, Siqing; Hermanowicz, Slawomir W.

2010-11-01

This study compared the whole composition of microbial communities in continuous-flow (MBR) and batch-fed (discontinuous) (MSBR) aerobic membrane bioreactors using high-density universal 16S rRNA Microarray. The array includes 506,944 probes targeted to 8935 clusters in 16S rRNA gene sequences. The Microarray results showed that both MBR and MSBR had high microbial diversity. 1126 and 1002 bacterial subfamilies were detected and can separate as 37 and 32 phyla in MBR and MSBR, respectively. Proteobacteria was the predominant phylum, 703 and 597 subfamilies were found in two systems, which constituted 62.4% and 59.6% of the whole bacteria. Gamma- and Alpha-were the dominant classes in Proteobacteria. It occupied 38.1% and 26.3%, 31.2% and 39.2% for MBR and MSBR, respectively. Bacteroidetes, Firmicutes and Actinobacteria were the subdominant groups, occupying around 9.4% and 7.6%, 6.1% and 6.5%, 6.0% and 9.0% of the total bacteria in two reactors. Some bacterial groups such as Acidobacteria, Chloroflexi, Cyanobacteria, Verrucomicrobia and Spirochaetes also found more than 15 subfamilies. All the results indicated that the MBR system had more bacteria community diversity than MSBR's. Moreover, it was very interested that MBR and MSBR had almost the same bacterial composition except Enterobacteriaceae. 63 OTUs of Enterobacteriaceae were detected in MBR, while just 10 OTUs were found in MSBR. That's one of the reasons leading to the difference of the bacterial diversity between two bioreactors.

Bacterial community in ancient permafrost alluvium at the Mammoth Mountain (Eastern Siberia).

PubMed

Brouchkov, Anatoli; Kabilov, Marsel; Filippova, Svetlana; Baturina, Olga; Rogov, Victor; Galchenko, Valery; Mulyukin, Andrey; Fursova, Oksana; Pogorelko, Gennady

2017-12-15

Permanently frozen (approx. 3.5Ma) alluvial Neogene sediments exposed in the Aldan river valley at the Mammoth Mountain (Eastern Siberia) are unique, ancient, and poorly studied permafrost environments. So far, the structure of the indigenous bacterial community has remained unknown. Use of 16S metagenomic analysis with total DNA isolation using DNA Spin Kit for Soil (MO-Bio) and QIAamp DNA Stool Mini Kit (Qiagen) has revealed the major and minor bacterial lineages in the permafrost alluvium sediments. In sum, 61 Operational Taxonomic Units (OTUs) with 31,239 reads (Qiagen kit) and 15,404 reads (Mo-Bio kit) could be assigned to the known taxa. Only three phyla, Bacteroidetes, Proteobacteria and Firmicutes, comprised >5% of the OTUs abundance and accounted for 99% of the total reads. OTUs pertaining to the top families (Chitinophagaceae, Caulobacteraceae, Sphingomonadaceae, Bradyrhizobiaceae, Halomonadaceae) held >90% of reads. The abundance of Actinobacteria was less (0.7%), whereas members of other phyla (Deinococcus-Thermus, Cyanobacteria/Chloroplast, Fusobacteria, and Acidobacteria) constituted a minor fraction of reads. The bacterial community in the studied ancient alluvium differs from other permafrost sediments, mainly by predominance of Bacteroidetes (>52%). The diversity of this preserved bacterial community has the potential to cause effects unknown if prompted to thaw and spread with changing climate. Therefore, this study elicits further reason to study how reintroduction of these ancient bacteria could affect the surrounding ecosystem, including current bacterial species. Copyright © 2017 Elsevier B.V. All rights reserved.

Understanding alternative fluxes/effluxes through comparative metabolic pathway analysis of phylum actinobacteria using a simplified approach.

PubMed

Verma, Mansi; Lal, Devi; Saxena, Anjali; Anand, Shailly; Kaur, Jasvinder; Kaur, Jaspreet; Lal, Rup

2013-12-01

Actinobacteria are known for their diverse metabolism and physiology. Some are dreadful human pathogens whereas some constitute the natural flora for human gut. Therefore, the understanding of metabolic pathways is a key feature for targeting the pathogenic bacteria without disturbing the symbiotic ones. A big challenge faced today is multiple drug resistance by Mycobacterium and other pathogens that utilize alternative fluxes/effluxes. With the availability of genome sequence, it is now feasible to conduct the comparative in silico analysis. Here we present a simplified approach to compare metabolic pathways so that the species specific enzyme may be traced and engineered for future therapeutics. The analyses of four key carbohydrate metabolic pathways, i.e., glycolysis, pyruvate metabolism, tri carboxylic acid cycle and pentose phosphate pathway suggest the presence of alternative fluxes. It was found that the upper pathway of glycolysis was highly variable in the actinobacterial genomes whereas lower glycolytic pathway was highly conserved. Likewise, pentose phosphate pathway was well conserved in contradiction to TCA cycle, which was found to be incomplete in majority of actinobacteria. The clustering based on presence and absence of genes of these metabolic pathways clearly revealed that members of different genera shared identical pathways and, therefore, provided an easy method to identify the metabolic similarities/differences between pathogenic and symbiotic organisms. The analyses could identify isoenzymes and some key enzymes that were found to be missing in some pathogenic actinobacteria. The present work defines a simple approach to explore the effluxes in four metabolic pathways within the phylum actinobacteria. The analysis clearly reflects that actinobacteria exhibit diverse routes for metabolizing substrates. The pathway comparison can help in finding the enzymes that can be used as drug targets for pathogens without effecting symbiotic organisms

Lantibiotics produced by Actinobacteria and their potential applications (a review).

PubMed

Gomes, Karen Machado; Duarte, Rafael Silva; de Freire Bastos, Maria do Carmo

2017-02-01

The phylum Actinobacteria, which comprises a great variety of Gram-positive bacteria with a high G+C content in their genomes, is known for its large production of bioactive compounds, including those with antimicrobial activity. Among the antimicrobials, bacteriocins, ribosomally synthesized peptides, represent an important arsenal of potential new drugs to face the increasing prevalence of resistance to antibiotics among microbial pathogens. The actinobacterial bacteriocins form a heterogeneous group of substances that is difficult to adapt to most proposed classification schemes. However, recent updates have accommodated efficiently the diversity of bacteriocins produced by this phylum. Among the bacteriocins, the lantibiotics represent a source of new antimicrobials to control infections caused mainly by Gram-positive bacteria and with a low propensity for resistance development. Moreover, some of these compounds have additional biological properties, exhibiting activity against viruses and tumour cells and having also potential to be used in blood pressure or inflammation control and in pain relief. Thus, lantibiotics already described in Actinobacteria exhibit potential practical applications in medical settings, food industry and agriculture, with examples at different stages of pre-clinical and clinical trials.

Termite nests as an abundant source of cultivable actinobacteria for biotechnological purposes.

PubMed

Sujada, Nikhom; Sungthong, Rungroch; Lumyong, Saisamorn

2014-01-01

A total of 118 actinobacterial isolates were collected from the three types of termite nests (mound, carton, and subterranean nests) to evaluate their potential as a source of bioactive actinobacteria with antimicrobial activity. The highest number (67 isolates) and generic abundance (7 known genera) of actinobacterial isolates were obtained from carton nests. Streptomyces was the dominant genus in each type of termite nest. In the non-Streptomyces group, Nocardia was the dominant genus detected in mound and carton nests, while Pseudonocardia was the dominant genus in subterranean nests. A discovery trend of novel species (<99% similarity in the 16S rRNA gene sequence) was also observed in the termite nests examined. Each type of termite nest housed >20% of bioactive actinobacteria that could inhibit the growth of at least one test organism, while 12 isolates, belonging to the genera Streptomyces, Amycolatopsis, Pseudonocardia, Micromonospora and Nocardia, exhibited distinct antimicrobial activities. Streptomyces sp. CMU-NKS-3 was the most distinct bioactive isolate. It was closely related to S. padanus MITKK-103T, which was confirmed by 99% similarities in their 16S rRNA gene sequences. The highest level of extracellular antimicrobial substances was produced by the isolate CMU-NKS-3, which was grown in potato dextrose broth and exhibited a wide range (6.10×10(-4)-1.25 mg mL(-1)) of minimum inhibitory concentrations against diverse pathogens. We concluded that termite nests are an abundant source of bioactive strains of cultivable actinobacteria for future biotechnological needs.

Termite Nests as an Abundant Source of Cultivable Actinobacteria for Biotechnological Purposes

PubMed Central

Sujada, Nikhom; Sungthong, Rungroch; Lumyong, Saisamorn

2014-01-01

A total of 118 actinobacterial isolates were collected from the three types of termite nests (mound, carton, and subterranean nests) to evaluate their potential as a source of bioactive actinobacteria with antimicrobial activity. The highest number (67 isolates) and generic abundance (7 known genera) of actinobacterial isolates were obtained from carton nests. Streptomyces was the dominant genus in each type of termite nest. In the non-Streptomyces group, Nocardia was the dominant genus detected in mound and carton nests, while Pseudonocardia was the dominant genus in subterranean nests. A discovery trend of novel species (<99% similarity in the 16S rRNA gene sequence) was also observed in the termite nests examined. Each type of termite nest housed >20% of bioactive actinobacteria that could inhibit the growth of at least one test organism, while 12 isolates, belonging to the genera Streptomyces, Amycolatopsis, Pseudonocardia, Micromonospora and Nocardia, exhibited distinct antimicrobial activities. Streptomyces sp. CMU-NKS-3 was the most distinct bioactive isolate. It was closely related to S. padanus MITKK-103T, which was confirmed by 99% similarities in their 16S rRNA gene sequences. The highest level of extracellular antimicrobial substances was produced by the isolate CMU-NKS-3, which was grown in potato dextrose broth and exhibited a wide range (6.10×10−4–1.25 mg mL−1) of minimum inhibitory concentrations against diverse pathogens. We concluded that termite nests are an abundant source of bioactive strains of cultivable actinobacteria for future biotechnological needs. PMID:24909709

Oral imazalil exposure induces gut microbiota dysbiosis and colonic inflammation in mice.

PubMed

Jin, Cuiyuan; Zeng, Zhaoyang; Fu, Zhengwei; Jin, Yuanxiang

2016-10-01

The fungicide imazalil (IMZ) is used extensively in vegetable and fruit plantations and as a post-harvest treatment to avoid rot. Here, we revealed that ingestion of 25, 50 and 100 mg IMZ kg(-1) body weight for 28 d induced gut microbiota dysbiosis and colonic inflammation in mice. The relative abundance of Bacteroidetes, Firmicutes and Actinobacteria in the cecal contents decreased significantly after exposure to 100 mg kg(-1) IMZ for 28 d. In feces, the relative abundance in Bacteroidetes, Firmicutes and Actinobacteria decreased significantly after being exposed to 100 mg kg(-1) IMZ for 1, 14 and 7 d, respectively. High throughput sequencing of the V3-V4 region of the bacterial 16S rRNA gene revealed a significant reduction in the richness and diversity of microbiota in cecal contents and feces of IMZ-treated mice. Operational taxonomic units (OTUs) analysis identified 49.3% of OTUs changed in cecal contents, while 55.6% of OTUs changed in the feces after IMZ exposure. Overall, at the phylum level, the relative abundance of Firmicutes, Proteobacteria and Actinobacteria increased and that of Bacteroidetes decreased in IMZ-treated groups. At the genus level, the abundance of Lactobacillus and Bifidobacterium decreased while those of Deltaproteobacteria and Desulfovibrio increased in response to IMZ exposure. In addition, it was observed that IMZ exposure could induce colonic inflammation characterized by infiltration of inflammatory cells, elevated levels of lipocalin-2 (lcn-2) in the feces, and increased mRNA levels of Tnf-α, IL-1β, IL-22 and IFN-γ in the colon. Our findings strongly suggest that ingestion of IMZ has some risks to human health. Copyright © 2016 Elsevier Ltd. All rights reserved.

High taxonomic diversity of cultivation-recalcitrant endophytic bacteria in grapevine field shoots, their in vitro introduction, and unsuspected persistence.

PubMed

Thomas, Pious; Sekhar, Aparna C; Shaik, Sadiq Pasha

2017-11-01

Molecular and microscopic analyses reveal enormous non-cultivable endophytic bacteria in grapevine field shoots with functional significance. Diverse bacteria enter tissue cultures through surface-sterilized tissues and survive surreptitiously with varying taxonomic realignments. The study was envisaged to assess the extent of endophytic bacterial association with field shoot tissues of grapevine and the likelihood of introduction of such internally colonizing bacteria in vitro adopting molecular techniques targeting the non-cultivable bacterial community. PowerFood ® -kit derived DNA from surface-sterilized field shoot tips of grapevine Flame Seedless was employed in a preliminary bacterial class-specific PCR screening proving positive for major prokaryotic taxa including Archaea. Taxonomic and functional diversity were analyzed through whole metagenome profiling (WMG) which revealed predominantly phylum Actinobacteria, Proteobacteria, and minor shares of Firmicutes, Bacteroidetes, and Deinococcus-Thermus with varying functional roles ascribable to the whole bacterial community. Field shoot tip tissues and callus derived from stem segments were further employed in 16S rRNA V3-V4 amplicon taxonomic profiling. This revealed elevated taxonomic diversity in field shoots over WMG, predominantly Proteobacteria succeeded by Actinobacteria, Firmicutes, Bacteroidetes, and 15 other phyla including several candidate phyla (135 families, 179 genera). Callus stocks also displayed broad bacterial diversity (16 phyla; 96 families; 141 genera) bearing resemblance to field tissues with Proteobacterial dominance but a reduction in its share, enrichment of Actinobacteria and Firmicutes, disappearance of some field-associated phyla and detection of a few additional taxonomic groups over field community. Similar results were documented during 16S V3-V4 amplicon taxonomic profiling on Thompson Seedless field shoot tip and callus tissues. Video microscopy on tissue homogenates

[New isolation methods and phylogenetic diversity of actinobacteria from hypersaline beach in Aksu].

PubMed

Zhang, Yao; Xia, Zhanfeng; Cao, Xinbo; Li, Jun; Zhang, Lili

2013-08-04

We explored 4 new methods to improve the isolation of actinobacterial resources from high salt areas. Optimized media based on 4 new strategies were used for isolating actinobacteria from hypersaline beaches. Glycerin-arginine, trehalose-creatine, glycerol-asparticacid, mannitol-casein, casein-mannitol, mannitol-alanine, chitosan-asparagineand GAUZE' No. 1 were used as basic media. New isolation strategy includes 4 methods: ten-fold dilution culture, simulation of the original environment, actinobacterial culture guided by uncultured molecular technology detected, and reference of actinobacterial media for brackish marine environment. The 16S rRNA genes of the isolates were amplified with bacterial universal primers. The results of 16S rRNA gene sequences were compared with sequences obtained from GenBank databases. We constructed phylogenetic tree with the neighbor-joining method. No actinobacterial strains were isolated by 8 media of control group, while 403 strains were isolated by new strategies. The isolates by new methods were members of 14 genera (Streptomyces, Streptomonospora, Saccharomonospora, Plantactinospora, Nocardia, Amycolatopsis, Glycomyces, Micromonospora, Nocardiopsis, Isoptericola, Nonomuraea, Thermobifida, Actinopolyspora, Actinomadura) of 10 families in 8 suborders. The most abundant and diverse isolates were the two suborders of Streptomycineae (69.96%) and Streptosporangineaesuborder (9.68%) within the phylum Actinobacteria, including 9 potential novel species. New isolation methods significantly improved the actinobacterial culturability of hypersaline areas, and obtained many potential novel species, which provided a new and more effective way to isolate actinobacteria resources in hypersaline environments.

Draft Genome Sequence of Microbacterium sp. Strain UCD-TDU (Phylum Actinobacteria)

PubMed Central

Bendiks, Zachary A.; Lang, Jenna M.; Darling, Aaron E.; Coil, David A.

2013-01-01

Here, we present the draft genome sequence of Microbacterium sp. strain UCD-TDU, a member of the phylum Actinobacteria. The assembly contains 3,746,321 bp (in 8 scaffolds). This strain was isolated from a residential toilet as part of an undergraduate student research project to sequence reference genomes of microbes from the built environment. PMID:23516225

Biofilm bacterial communities in urban drinking water distribution systems transporting waters with different purification strategies.

PubMed

Wu, Huiting; Zhang, Jingxu; Mi, Zilong; Xie, Shuguang; Chen, Chao; Zhang, Xiaojian

2015-02-01

Biofilm formation in drinking water distribution systems (DWDS) has many adverse consequences. Knowledge of microbial community structure of DWDS biofilm can aid in the design of an effective control strategy. However, biofilm bacterial community in real DWDS and the impact of drinking water purification strategy remain unclear. The present study investigated the composition and diversity of biofilm bacterial community in real DWDSs transporting waters with different purification strategies (conventional treatment and integrated treatment). High-throughput Illumina MiSeq sequencing analysis illustrated a large shift in the diversity and structure of biofilm bacterial community in real DWDS. Proteobacteria, Firmicutes, Bacteroidetes, Actinobacteria, Nitrospirae, and Cyanobacteria were the major components of biofilm bacterial community. Proteobacteria (mainly Alphaproteobacteria, Betaproteobacteria, and Gammaproteobacteria) predominated in each DWDS biofilm, but the compositions of the dominant proteobacterial classes and genera and their proportions varied among biofilm samples. Drinking water purification strategy could shape DWDS biofilm bacterial community. Moreover, Pearson's correlation analysis indicated that Actinobacteria was positively correlated with the levels of total alkalinity and dissolved organic carbon in tap water, while Firmicutes had a significant positive correlation with nitrite nitrogen.

Bioprospection of actinobacteria derived from freshwater sediments for their potential to produce antimicrobial compounds.

PubMed

Zothanpuia; Passari, Ajit Kumar; Leo, Vincent Vineeth; Chandra, Preeti; Kumar, Brijesh; Nayak, Chandra; Hashem, Abeer; Abd Allah, Elsayed Fathi; Alqarawi, Abdulaziz A; Singh, Bhim Pratap

2018-05-05

Actinobacteria from freshwater habitats have been explored less than from other habitats in the search for compounds of pharmaceutical value. This study highlighted the abundance of actinobacteria from freshwater sediments of two rivers and one lake, and the isolates were studied for their ability to produce antimicrobial bioactive compounds. 16S rRNA gene sequencing led to the identification of 84 actinobacterial isolates separated into a common genus (Streptomyces) and eight rare genera (Nocardiopsis, Saccharopolyspora, Rhodococcus, Prauserella, Amycolatopsis, Promicromonospora, Kocuria and Micrococcus). All strains that showed significant inhibition potentials were found against Gram-positive, Gram-negative and yeast pathogens. Further, three biosynthetic genes, polyketide synthases type II (PKS II), nonribosomal peptide synthetases (NRPS) and aminodeoxyisochorismate synthase (phzE), were detected in 38, 71 and 29% of the strains, respectively. Six isolates based on their antimicrobial potentials were selected for the detection and quantification of standard antibiotics using ultra performance liquid chromatography (UPLC-ESI-MS/MS) and volatile organic compounds (VOCs) using gas chromatography mass spectrometry (GC/MS). Four antibiotics (fluconazole, trimethoprim, ketoconazole and rifampicin) and 35 VOCs were quantified and determined from the methanolic crude extract of six selected Streptomyces strains. Infectious diseases still remain one of the leading causes of death globally and bacterial infections caused millions of deaths annually. Culturable actinobacteria associated with freshwater lake and river sediments has the prospects for the production of bioactive secondary metabolites.

Isolation and screening of rare Actinobacteria, a new insight for finding natural products with antivascular calcification activity.

PubMed

Salimi, F; Hamedi, J; Motevaseli, E; Mohammadipanah, F

2018-01-01

Vascular calcification (VC) is a significant pathological process in some life-threatening diseases. Several pathological mechanisms, including transdifferentiation of vascular smooth muscle cells to osteoblast-like cells and apoptosis are involved in VC. Compounds with an inhibitory effect on these processes are potentially efficient medications. In consideration of the multiple biological activities of Actinobacteria, this research was aimed at finding anti-VC metabolite-producing Actinobacteria. After the isolation and identification of Actinobacteria, the effect of their fermentation broth extracts on the apoptosis rate was measured using various methods, for example, ethidium bromide/acridine orange staining, DNA laddering and diphenylamine assays. The effect of the most effective fermentation broth extract of Actinobacteria (FBEA) on the mRNA expression of runt-related transcription factor 2 (Runx2) and osteopontin (OPN) was examined. Finally, the most effective FBEA was fractionated and the chemical composition of anti-VC fractions was analysed using GC-MS. Various VC inhibition rates were observed in the tested FBEA (20 μg ml -1 ; 17·9-60·15%). The inhibition of DNA fragmentation was 7-48%. The FBE with the greatest anticalcification activity belonged to Kribbella sp. UTMC 267 and, according to 16S rRNA analysis, Kribbella sancticallisti with a similarity of 98·53% is its nearest neighbour. The FBE of Kribbella sp. UTMC 267 reduced Runx2 mRNA expression by 2·95-fold and OPN mRNA expression by 28·57-fold, both of which are considered significant (P < 0·05). Finally, GC-MS analysis showed the existence of potent anti-oxidative and anti-inflammation agents in FBE of Kribbella sp. UTMC 267. Actinobacterial metabolites can provide a new strategy for treating VC diseases by reducing the expression of osteogenic genes, the apoptosis rate and oxidative stress. This study highlights the therapeutic potential of Kribbella sp. metabolites and Actinobacteria

The diversity and antibiotic properties of actinobacteria associated with endemic deepwater amphipods of Lake Baikal.

PubMed

Protasov, Eugenii S; Axenov-Gribanov, Denis V; Rebets, Yuriy V; Voytsekhovskaya, Irina V; Tokovenko, Bogdan T; Shatilina, Zhanna M; Luzhetskyy, Andriy N; Timofeyev, Maxim A

2017-12-01

The emergence of pathogenic bacteria resistant to antibiotics increases the need for discovery of new effective antimicrobials. Unique habitats such as marine deposits, wetlands and caves or unexplored biological communities are promising sources for the isolation of actinobacteria, which are among the major antibiotic producers. The present study aimed at examining cultivated actinobacteria strains associated with endemic Lake Baikal deepwater amphipods and estimating their antibiotic activity. We isolated 42 actinobacterial strains from crustaceans belonging to Ommatogammarus albinus and Ommatogammarus flavus. To our knowledge, this is the first report describing the isolation and initial characterization of representatives of Micromonospora and Pseudonocardia genera from Baikal deepwater invertebrates. Also, as expected, representatives of the genus Streptomyces were the dominant group among the isolated species. Some correlations could be observed between the number of actinobacterial isolates, the depth of sampling and the source of the strains. Nevertheless, >70% of isolated strains demonstrated antifungal activity. The dereplication analysis of extract of one of the isolated strains resulted in annotation of several known compounds that can help to explain the observed biological activities. The characteristics of ecological niche and lifestyle of deepwater amphipods suggests that the observed associations between crustaceans and isolated actinobacteria are not random and might represent long-term symbiotic interactions.

The Cyanobacteria-Dominated Sponge Dactylospongia elegans in the South China Sea: Prokaryotic Community and Metagenomic Insights.

PubMed

Gao, Zhao-Ming; Zhou, Guo-Wei; Huang, Hui; Wang, Yong

2017-01-01

The South China Sea is a special reservoir of sponges of which prokaryotic communities are less studied. Here, a new record of the sponge Dactylospongia elegans is reported near the coast of Jinqing Island in the South China Sea, and its prokaryotic community is comprehensively investigated. Sponge specimens displayed lower microbial diversity compared with surrounding seawater. At the phylum level, prokaryotic communities were consistently dominated by Proteobacteria, followed by Cyanobacteria, Chloroflexi, Acidobacteria, Actinobacteria, Gemmatimonadetes, Thaumarchaeota, and Poribacteria. Operational taxonomic unit (OTU) analysis alternatively showed that the most abundant symbiont was the sponge-specific cyanobacterial species " Candidatus Synechococcus spongiarum," followed by OTUs belonging to the unidentified Chloroflexi and Acidobacteria. Phylogenetic tree based on 16S-23S internal transcribed spacer regions indicated that the dominated cyanobacterial OTU represented a new clade of " Ca . Synechococcus spongiarum." More reliable metagenomic data further revealed that poribacterial symbionts were highly abundant and only secondary to the cyanobacterial symbiont. One draft genome for each of the Cyanobacteria, Chloroflexi and Acidobacteria and three poribacterial genomes were extracted from the metagenomes. Among them, genomes affiliated with the Chloroflexi and Acidobacteria were reported for the first time in sponge symbionts. Eukaryotic-like domains were found in all the binned genomes, indicating their potential symbiotic roles with the sponge host. The high quality of the six recovered genomes of sponge symbionts from the sponge D. elegans makes it possible to understand their symbiotic roles and interactions with the sponge host as well as among one another.

Isolation and characterization of anti-adenoviral secondary metabolites from marine actinobacteria.

PubMed

Strand, Mårten; Carlsson, Marcus; Uvell, Hanna; Islam, Koushikul; Edlund, Karin; Cullman, Inger; Altermark, Björn; Mei, Ya-Fang; Elofsson, Mikael; Willassen, Nils-Peder; Wadell, Göran; Almqvist, Fredrik

2014-01-28

Adenovirus infections in immunocompromised patients are associated with high mortality rates. Currently, there are no effective anti-adenoviral therapies available. It is well known that actinobacteria can produce secondary metabolites that are attractive in drug discovery due to their structural diversity and their evolved interaction with biomolecules. Here, we have established an extract library derived from actinobacteria isolated from Vestfjorden, Norway, and performed a screening campaign to discover anti-adenoviral compounds. One extract with anti-adenoviral activity was found to contain a diastereomeric 1:1 mixture of the butenolide secondary alcohols 1a and 1b. By further cultivation and analysis, we could isolate 1a and 1b in different diastereomeric ratio. In addition, three more anti-adenoviral butenolides 2, 3 and 4 with differences in their side-chains were isolated. In this study, the anti-adenoviral activity of these compounds was characterized and substantial differences in the cytotoxic potential between the butenolide analogs were observed. The most potent butenolide analog 3 displayed an EC50 value of 91 μM and no prominent cytotoxicity at 2 mM. Furthermore, we propose a biosynthetic pathway for these compounds based on their relative time of appearance and structure.

The Arctic Soil Bacterial Communities in the Vicinity of a Little Auk Colony

PubMed Central

Zielińska, Sylwia; Kidawa, Dorota; Stempniewicz, Lech; Łoś, Marcin; Łoś, Joanna M.

2016-01-01

Due to deposition of birds' guano, eggshells or feathers, the vicinity of a large seabirds' breeding colony is expected to have a substantial impact on the soil's physicochemical features as well as on diversity of vegetation and the soil invertebrates. Consequently, due to changing physicochemical features the structure of bacterial communities might fluctuate in different soil environments. The aim of this study was to investigate the bacterial assemblages in the Arctic soil within the area of a birds' colony and in a control sample from a topographically similar location but situated away from the colony's impact area. A high number of OTUs found in both areas indicates a highly complex microbial populations structure. The most abundant phyla in both of the tested samples were: Proteobacteria, Acidobacteria, Actinobacteria, and Chloroflexi, with different proportions in the total share. Despite differences in the physicochemical soil characteristics, the soil microbial community structures at the phylum level were similar to some extent in the two samples. The only share that was significantly higher in the control area when compared to the sample obtained within the birds' colony, belonged to the Actinobacteria phylum. Moreover, when analyzing the class level for each phylum, several differences between the samples were observed. Furthermore, lower proportions of Proteobacteria and Acidobacteria were observed in the soil sample under the influence of the bird's colony, which most probably could be linked to higher nitrogen concentrations in that sample. PMID:27667982

Potential for biocontrol of melanized fungi by actinobacteria isolated from intertidal region of Ilha Do Mel, Paraná, Brazil.

PubMed

Dalitz, Camila de Araújo; Porsani, Mariana Vieira; Figel, Izabel Cristina; Pimentel, Ida C; Dalzoto, Patrícia R

Actinobacteria occur in many environments and have the capacity to produce secondary metabolites with antibiotic potential. Identification and taxonomy of actinobacteria that produce antimicrobial substances is essential for the screening of new compounds, and sequencing of the 16S region of ribosomal DNA (rDNA), which is conserved and present in all bacteria, is an important method of identification. Melanized fungi are free-living organisms, which can also be pathogens of clinical importance. This work aimed to evaluate growth inhibition of melanized fungi by actinobacteria and to identify the latter to the species level. In this study, antimicrobial activity of 13 actinobacterial isolates from the genus Streptomyces was evaluated against seven melanized fungi of the genera Exophiala, Cladosporium, and Rhinocladiella. In all tests, all actinobacterial isolates showed inhibitory activity against all isolates of melanized fungi, and only one actinobacterial isolate had less efficient inhibitory activity. The 16S rDNA region of five previously unidentified actinobacterial isolates from Ilha do Mel, Paraná, Brazil, was sequenced; four of the isolates were identified as Streptomyces globisporus subsp. globisporus, and one isolate was identified as Streptomyces aureus. This work highlights the potential of actinobacteria with antifungal activity and their role in the pursuit of novel antimicrobial substances. Copyright © 2016 Sociedade Brasileira de Microbiologia. Published by Elsevier Editora Ltda. All rights reserved.

Sequence-based identification of inositol monophosphatase-like histidinol-phosphate phosphatases (HisN) in Corynebacterium glutamicum, Actinobacteria, and beyond.

PubMed

Kulis-Horn, Robert Kasimir; Rückert, Christian; Kalinowski, Jörn; Persicke, Marcus

2017-07-18

The eighth step of L-histidine biosynthesis is carried out by an enzyme called histidinol-phosphate phosphatase (HolPase). Three unrelated HolPase families are known so far. Two of them are well studied: HAD-type HolPases known from Gammaproteobacteria like Escherichia coli or Salmonella enterica and PHP-type HolPases known from yeast and Firmicutes like Bacillus subtilis. However, the third family of HolPases, the inositol monophosphatase (IMPase)-like HolPases, present in Actinobacteria like Corynebacterium glutamicum (HisN) and plants, are poorly characterized. Moreover, there exist several IMPase-like proteins in bacteria (e.g. CysQ, ImpA, and SuhB) which are very similar to HisN but most likely do not participate in L-histidine biosynthesis. Deletion of hisN, the gene encoding the IMPase-like HolPase in C. glutamicum, does not result in complete L-histidine auxotrophy. Out of four hisN homologs present in the genome of C. glutamicum (impA, suhB, cysQ, and cg0911), only cg0911 encodes an enzyme with HolPase activity. The enzymatic properties of HisN and Cg0911 were determined, delivering the first available kinetic data for IMPase-like HolPases. Additionally, we analyzed the amino acid sequences of potential HisN, ImpA, SuhB, CysQ and Cg0911 orthologs from bacteria and identified six conserved sequence motifs for each group of orthologs. Mutational studies confirmed the importance of a highly conserved aspartate residue accompanied by several aromatic amino acid residues present in motif 5 for HolPase activity. Several bacterial proteins containing all identified HolPase motifs, but showing only moderate sequence similarity to HisN from C. glutamicum, were experimentally confirmed as IMPase-like HolPases, demonstrating the value of the identified motifs. Based on the confirmed IMPase-like HolPases two profile Hidden Markov Models (HMMs) were build using an iterative approach. These HMMs allow the fast, reliable detection and differentiation of the two

Abiotic factors shape microbial diversity in Sonoran Desert soils.

PubMed

Andrew, David R; Fitak, Robert R; Munguia-Vega, Adrian; Racolta, Adriana; Martinson, Vincent G; Dontsova, Katerina

2012-11-01

High-throughput, culture-independent surveys of bacterial and archaeal communities in soil have illuminated the importance of both edaphic and biotic influences on microbial diversity, yet few studies compare the relative importance of these factors. Here, we employ multiplexed pyrosequencing of the 16S rRNA gene to examine soil- and cactus-associated rhizosphere microbial communities of the Sonoran Desert and the artificial desert biome of the Biosphere2 research facility. The results of our replicate sampling approach show that microbial communities are shaped primarily by soil characteristics associated with geographic locations, while rhizosphere associations are secondary factors. We found little difference between rhizosphere communities of the ecologically similar saguaro (Carnegiea gigantea) and cardón (Pachycereus pringlei) cacti. Both rhizosphere and soil communities were dominated by the disproportionately abundant Crenarchaeota class Thermoprotei, which comprised 18.7% of 183,320 total pyrosequencing reads from a comparatively small number (1,337 or 3.7%) of the 36,162 total operational taxonomic units (OTUs). OTUs common to both soil and rhizosphere samples comprised the bulk of raw sequence reads, suggesting that the shared community of soil and rhizosphere microbes constitute common and abundant taxa, particularly in the bacterial phyla Proteobacteria, Actinobacteria, Planctomycetes, Firmicutes, Bacteroidetes, Chloroflexi, and Acidobacteria. The vast majority of OTUs, however, were rare and unique to either soil or rhizosphere communities and differed among locations dozens of kilometers apart. Several soil properties, particularly soil pH and carbon content, were significantly correlated with community diversity measurements. Our results highlight the importance of culture-independent approaches in surveying microbial communities of extreme environments.

Taxonomic and functional characteristics of microbial communities and their correlation with physicochemical properties of four geothermal springs in Odisha, India

PubMed Central

Badhai, Jhasketan; Ghosh, Tarini S.; Das, Subrata K.

2015-01-01

This study describes microbial diversity in four tropical hot springs representing moderately thermophilic environments (temperature range: 40–58°C; pH: 7.2–7.4) with discrete geochemistry. Metagenome sequence data showed a dominance of Bacteria over Archaea; the most abundant phyla were Chloroflexi and Proteobacteria, although other phyla were also present, such as Acetothermia, Nitrospirae, Acidobacteria, Firmicutes, Deinococcus-Thermus, Bacteroidetes, Thermotogae, Euryarchaeota, Verrucomicrobia, Ignavibacteriae, Cyanobacteria, Actinobacteria, Planctomycetes, Spirochaetes, Armatimonadetes, Crenarchaeota, and Aquificae. The distribution of major genera and their statistical correlation analyses with the physicochemical parameters predicted that the temperature, aqueous concentrations of ions (such as sodium, chloride, sulfate, and bicarbonate), total hardness, dissolved solids and conductivity were the main environmental variables influencing microbial community composition and diversity. Despite the observed high taxonomic diversity, there were only little variations in the overall functional profiles of the microbial communities in the four springs. Genes involved in the metabolism of carbohydrates and carbon fixation were the most abundant functional class of genes present in these hot springs. The distribution of genes involved in carbon fixation predicted the presence of all the six known autotrophic pathways in the metagenomes. A high prevalence of genes involved in membrane transport, signal transduction, stress response, bacterial chemotaxis, and flagellar assembly were observed along with genes involved in the pathways of xenobiotic degradation and metabolism. The analysis of the metagenomic sequences affiliated to the candidate phylum Acetothermia from spring TB-3 provided new insight into the metabolism and physiology of yet-unknown members of this lineage of bacteria. PMID:26579081

Taxonomic and functional characteristics of microbial communities and their correlation with physicochemical properties of four geothermal springs in Odisha, India.

PubMed

Badhai, Jhasketan; Ghosh, Tarini S; Das, Subrata K

2015-01-01

This study describes microbial diversity in four tropical hot springs representing moderately thermophilic environments (temperature range: 40-58°C; pH: 7.2-7.4) with discrete geochemistry. Metagenome sequence data showed a dominance of Bacteria over Archaea; the most abundant phyla were Chloroflexi and Proteobacteria, although other phyla were also present, such as Acetothermia, Nitrospirae, Acidobacteria, Firmicutes, Deinococcus-Thermus, Bacteroidetes, Thermotogae, Euryarchaeota, Verrucomicrobia, Ignavibacteriae, Cyanobacteria, Actinobacteria, Planctomycetes, Spirochaetes, Armatimonadetes, Crenarchaeota, and Aquificae. The distribution of major genera and their statistical correlation analyses with the physicochemical parameters predicted that the temperature, aqueous concentrations of ions (such as sodium, chloride, sulfate, and bicarbonate), total hardness, dissolved solids and conductivity were the main environmental variables influencing microbial community composition and diversity. Despite the observed high taxonomic diversity, there were only little variations in the overall functional profiles of the microbial communities in the four springs. Genes involved in the metabolism of carbohydrates and carbon fixation were the most abundant functional class of genes present in these hot springs. The distribution of genes involved in carbon fixation predicted the presence of all the six known autotrophic pathways in the metagenomes. A high prevalence of genes involved in membrane transport, signal transduction, stress response, bacterial chemotaxis, and flagellar assembly were observed along with genes involved in the pathways of xenobiotic degradation and metabolism. The analysis of the metagenomic sequences affiliated to the candidate phylum Acetothermia from spring TB-3 provided new insight into the metabolism and physiology of yet-unknown members of this lineage of bacteria.

Bacterial community composition in different sediments from the Eastern Mediterranean Sea: a comparison of four 16S ribosomal DNA clone libraries.

PubMed

Polymenakou, Paraskevi N; Bertilsson, Stefan; Tselepides, Anastasios; Stephanou, Euripides G

2005-10-01

The regional variability of sediment bacterial community composition and diversity was studied by comparative analysis of four large 16S ribosomal DNA (rDNA) clone libraries from sediments in different regions of the Eastern Mediterranean Sea (Thermaikos Gulf, Cretan Sea, and South lonian Sea). Amplified rDNA restriction analysis of 664 clones from the libraries indicate that the rDNA richness and evenness was high: for example, a near-1:1 relationship among screened clones and number of unique restriction patterns when up to 190 clones were screened for each library. Phylogenetic analysis of 207 bacterial 16S rDNA sequences from the sediment libraries demonstrated that Gamma-, Delta-, and Alphaproteobacteria, Holophaga/Acidobacteria, Planctomycetales, Actinobacteria, Bacteroidetes, and Verrucomicrobia were represented in all four libraries. A few clones also grouped with the Betaproteobacteria, Nitrospirae, Spirochaetales, Chlamydiae, Firmicutes, and candidate division OPl 1. The abundance of sequences affiliated with Gammaproteobacteria was higher in libraries from shallow sediments in the Thermaikos Gulf (30 m) and the Cretan Sea (100 m) compared to the deeper South Ionian station (2790 m). Most sequences in the four sediment libraries clustered with uncultured 16S rDNA phylotypes from marine habitats, and many of the closest matches were clones from hydrocarbon seeps, benzene-mineralizing consortia, sulfate reducers, sulk oxidizers, and ammonia oxidizers. LIBSHUFF statistics of 16S rDNA gene sequences from the four libraries revealed major differences, indicating either a very high richness in the sediment bacterial communities or considerable variability in bacterial community composition among regions, or both.

Acidicapsa ferrireducens sp. nov., Acidicapsa acidiphila sp. nov., and Granulicella acidiphila sp. nov.: novel acidobacteria isolated from metal-rich acidic waters.

PubMed

Falagán, Carmen; Foesel, Bärbel; Johnson, Barrie

2017-05-01

Four novel strains of Acidobacteria were isolated from water samples taken from pit lakes at two abandoned metal mines in the Iberian Pyrite Belt mining district, south-west Spain. Three of the isolates belong to the genus Acidicapsa (MCF9 T , MCF10 T , and MCF14) and one of them to the genus Granulicella (MCF40 T ). All isolates are moderately acidophilic (pH growth optimum 3.8-4.1) and mesophilic (temperature growth optima 30-32 °C). Isolates MCF10 T and MCF40 T grew at pH lower (<3.0) than previously reported for all other acidobacteria. All four strains are obligate heterotrophs and metabolised a wide range of sugars. While all four isolates are obligate aerobes, MCF9 T , MCF10 T , and MCF14 catalysed the reductive dissolution of the ferric iron mineral schwertmannite when incubated under micro-aerobic conditions. Isolates MCF9 T and MCF14 shared 99.5% similarity of their 16 S rRNA genes, and were considered to be strains of the same species. The major quinone of strains MCF10 T , MCF9 T , and MCF40 T is MK-8, and their DNA G + C contents are 60.0, 59.7, and 62.1 mol%, respectively. Based on phylogenetic and phenotypic data, three novel species, Acidicapsa ferrireducens strain MCF9 T (=DSM 28997 T  = NCCB 100575 T ), Acidicapsa acidiphila strain MCF10 T (=DSM 29819 T  = NCCB 100576 T ), and Granulicella acidiphila strain MCF40 T (DSM 28996 T  = NCCB 100577 T ), are proposed.

Microbial Flora Associated with the Halophyte–Salsola imbricate and Its Biotechnical Potential

PubMed Central

Bibi, Fehmida; Strobel, Gary A.; Naseer, Muhammad I.; Yasir, Muhammad; Khalaf Al-Ghamdi, Ahmed A.; Azhar, Esam I.

2018-01-01

Halophytes are associated with the intertidal forest ecosystem of Saudi Arabia and seemingly have an immense potential for yielding useful and important natural products. In this study we have aimed to isolate and characterize the endophytic and rhizospheric bacterial communities from the halophyte, Salsola imbricata, In addition these bacterial strains were identified and selected strains were further studied for bioactive secondary metabolites. At least 168 rhizspheric and endophytic bacteria were isolated and of these 22 were active antagonists against the oomycetous fungal plant pathogens, Phytophthora capsici and Pythium ultimum. Active cultures were mainly identified with molecular techniques (16S r DNA) and this revealed 95.7–100% sequence similarities with relevant type strains. These microorgansims were grouped into four major classes: Actinobacteria, Firmicutes, β-Proteobacteria, and γ-Proteobacteria. Production of fungal cell wall lytic enzymes was detected mostly in members of Actinobacteria and Firmicutes. PCR screening for type I polyketide synthases (PKS-I), type II polyketide synthases (PKS-II) and nonribosomal peptide synthetases (NRPS) revealed 13 of the 22 strains (59%) were positive for at least one of these important biosynthetic genes that are known to be involved in the synthesis of important antibiotics. Four bacterial strains of Actinobacteria with potential antagonistic activity including two rhizobacteria, EA52 (Nocardiopsis sp.), EA58 (Pseudonocardia sp.) and two endophytic bacteria Streptomyces sp. (EA65) and Streptomyces sp. (EA67) were selected for secondary metabolite analyses using LC-MS. As a result, the presence of different bioactive compounds in the culture extracts was detected some of which are already reported for their diverse biological activities including antibiotics such as Sulfamethoxypyridazine, Sulfamerazine, and Dimetridazole. In conclusion, this study provides an insight into antagonistic bacterial population

Bacterial community changes in response to oil contamination and perennial crop cultivation.

PubMed

Yan, Lijuan; Penttinen, Petri; Mikkonen, Anu; Lindström, Kristina

2018-05-01

We investigated bacterial community dynamics in response to used motor oil contamination and perennial crop cultivation by 16S rRNA gene amplicon sequencing in a 4-year field study. Actinobacteria, Proteobacteria, Chloroflexi, Acidobacteria, and Gemmatimonadetes were the major bacterial phyla, and Rhodococcus was the most abundant genus. Initially, oil contamination decreased the overall bacterial diversity. Actinobacteria, Betaproteobacteria, and Gammaproteobacteria were sensitive to oil contamination, exhibiting clear succession with time. However, bacterial communities changed over time, regardless of oil contamination and crop cultivation. The abundance difference of most OTUs between oil-contaminated and non-contaminated plots remained the same in later sampling years after the initial abundance difference induced by oil spike. The abundances of three oil-favored actinobacteria (Lysinimonas, Microbacteriaceae, and Marmoricola) and one betaproteobacterium (Aquabacterium) changed in different manner over time in oil-contaminated and non-contaminated soil. We propose that these taxa are potential bio-indicators for monitoring recovery from motor oil contamination in boreal soil. The effect of crop cultivation on bacterial communities became significant only after the crops achieved stable growth, likely associated with plant material decomposition by Bacteroidetes, Armatimonadetes and Fibrobacteres.

The Cyanobacteria-Dominated Sponge Dactylospongia elegans in the South China Sea: Prokaryotic Community and Metagenomic Insights

PubMed Central

Gao, Zhao-Ming; Zhou, Guo-Wei; Huang, Hui; Wang, Yong

2017-01-01

The South China Sea is a special reservoir of sponges of which prokaryotic communities are less studied. Here, a new record of the sponge Dactylospongia elegans is reported near the coast of Jinqing Island in the South China Sea, and its prokaryotic community is comprehensively investigated. Sponge specimens displayed lower microbial diversity compared with surrounding seawater. At the phylum level, prokaryotic communities were consistently dominated by Proteobacteria, followed by Cyanobacteria, Chloroflexi, Acidobacteria, Actinobacteria, Gemmatimonadetes, Thaumarchaeota, and Poribacteria. Operational taxonomic unit (OTU) analysis alternatively showed that the most abundant symbiont was the sponge-specific cyanobacterial species “Candidatus Synechococcus spongiarum,” followed by OTUs belonging to the unidentified Chloroflexi and Acidobacteria. Phylogenetic tree based on 16S-23S internal transcribed spacer regions indicated that the dominated cyanobacterial OTU represented a new clade of “Ca. Synechococcus spongiarum.” More reliable metagenomic data further revealed that poribacterial symbionts were highly abundant and only secondary to the cyanobacterial symbiont. One draft genome for each of the Cyanobacteria, Chloroflexi and Acidobacteria and three poribacterial genomes were extracted from the metagenomes. Among them, genomes affiliated with the Chloroflexi and Acidobacteria were reported for the first time in sponge symbionts. Eukaryotic-like domains were found in all the binned genomes, indicating their potential symbiotic roles with the sponge host. The high quality of the six recovered genomes of sponge symbionts from the sponge D. elegans makes it possible to understand their symbiotic roles and interactions with the sponge host as well as among one another. PMID:28790992

Pyrosequencing-based assessment of the bacteria diversity in surface and subsurface peat layers of a northern wetland, with focus on poorly studied phyla and candidate divisions.

PubMed

Serkebaeva, Yulia M; Kim, Yongkyu; Liesack, Werner; Dedysh, Svetlana N

2013-01-01

Northern peatlands play a key role in the global carbon and water budget, but the bacterial diversity in these ecosystems remains poorly described. Here, we compared the bacterial community composition in the surface (0-5 cm depth) and subsurface (45-50 cm) peat layers of an acidic (pH 4.0) Sphagnum-dominated wetland, using pyrosequencing of 16S rRNA genes. The denoised sequences (37,229 reads, average length ∼430 bp) were affiliated with 27 bacterial phyla and corresponded to 1,269 operational taxonomic units (OTUs) determined at 97% sequence identity. Abundant OTUs were affiliated with the Acidobacteria (35.5±2.4% and 39.2±1.2% of all classified sequences in surface and subsurface peat, respectively), Alphaproteobacteria (15.9±1.7% and 25.8±1.4%), Actinobacteria (9.5±2.0% and 10.7±0.5%), Verrucomicrobia (8.5±1.4% and 0.6±0.2%), Planctomycetes (5.8±0.4% and 9.7±0.6%), Deltaproteobacteria (7.1±0.4% and 4.4%±0.3%), and Gammaproteobacteria (6.6±0.4% and 2.1±0.1%). The taxonomic patterns of the abundant OTUs were uniform across all the subsamples taken from each peat layer. In contrast, the taxonomic patterns of rare OTUs were different from those of the abundant OTUs and varied greatly among subsamples, in both surface and subsurface peat. In addition to the bacterial taxa listed above, rare OTUs represented the following groups: Armatimonadetes, Bacteroidetes, Chlamydia, Chloroflexi, Cyanobacteria, Elusimicrobia, Fibrobacteres, Firmicutes, Gemmatimonadetes, Spirochaetes, AD3, WS1, WS4, WS5, WYO, OD1, OP3, BRC1, TM6, TM7, WPS-2, and FCPU426. OTU richness was notably higher in the surface layer (882 OTUs) than in the anoxic subsurface peat (483 OTUs), with only 96 OTUs common to both data sets. Most members of poorly studied phyla, such as the Acidobacteria, Verrucomicrobia, Planctomycetes and the candidate division TM6, showed a clear preference for growth in either oxic or anoxic conditions. Apparently, the bacterial communities in surface and

Pharmacological Potential of Phylogenetically Diverse Actinobacteria Isolated from Deep-Sea Coral Ecosystems of the Submarine Avilés Canyon in the Cantabrian Sea.

PubMed

Sarmiento-Vizcaíno, Aida; González, Verónica; Braña, Alfredo F; Palacios, Juan J; Otero, Luis; Fernández, Jonathan; Molina, Axayacatl; Kulik, Andreas; Vázquez, Fernando; Acuña, José L; García, Luis A; Blanco, Gloria

2017-02-01

Marine Actinobacteria are emerging as an unexplored source for natural product discovery. Eighty-seven deep-sea coral reef invertebrates were collected during an oceanographic expedition at the submarine Avilés Canyon (Asturias, Spain) in a range of 1500 to 4700 m depth. From these, 18 cultivable bioactive Actinobacteria were isolated, mainly from corals, phylum Cnidaria, and some specimens of phyla Echinodermata, Porifera, Annelida, Arthropoda, Mollusca and Sipuncula. As determined by 16S rRNA sequencing and phylogenetic analyses, all isolates belong to the phylum Actinobacteria, mainly to the Streptomyces genus and also to Micromonospora, Pseudonocardia and Myceligenerans. Production of bioactive compounds of pharmacological interest was investigated by high-performance liquid chromatography (HPLC) and gas chromatography-mass spectrometry (GC-MS) techniques and subsequent database comparison. Results reveal that deep-sea isolated Actinobacteria display a wide repertoire of secondary metabolite production with a high chemical diversity. Most identified products (both diffusible and volatiles) are known by their contrasted antibiotic or antitumor activities. Bioassays with ethyl acetate extracts from isolates displayed strong antibiotic activities against a panel of important resistant clinical pathogens, including Gram-positive and Gram-negative bacteria, as well as fungi, all of them isolated at two main hospitals (HUCA and Cabueñes) from the same geographical region. The identity of the active extracts components of these producing Actinobacteria is currently being investigated, given its potential for the discovery of pharmaceuticals and other products of biotechnological interest.

UV-Resistant Actinobacteria from High-Altitude Andean Lakes: Isolation, Characterization and Antagonistic Activities.

PubMed

Rasuk, María Cecilia; Ferrer, Gabriela Mónica; Kurth, Daniel; Portero, Luciano Raúl; Farías, María Eugenia; Albarracín, Virginia Helena

2017-05-01

Polyextremophiles are present in a wide variety of extreme environments in which they must overcome various hostile conditions simultaneously such as high UVB radiation, extreme pHs and temperatures, elevated salt and heavy-metal concentration, low-oxygen pressure and scarce nutrients. High-altitude Andean lakes (HAALs; between 2000 and 4000 m) are one example of these kinds of ecosystems suffering from the highest total solar and UVB radiation on Earth where an abundant and diverse polyextremophilic microbiota was reported. In this work, we performed the first extensive isolation of UV-resistant actinobacteria from soils, water, sediments and modern stromatolites at HAALs. Based on the 16S rRNA sequence, the strains were identified as members of the genera Streptomyces, Micrococcus, Nesterenkonia, Rhodococcus, Microbacterium, Kocuria, Arthrobacter, Micromonospora, Blastococcus, Citrococcus and Brevibacterium. Most isolates displayed resistance to multiple environmental stress factors confirming their polyextremophilic nature and were able to produce effective antimicrobial compounds. HAALs constitute a largely unexplored repository of UV-resistant actinobacteria, with high potential for the biodiscovery of novel natural products. © 2017 The American Society of Photobiology.

Genetic and functional characterization of culturable plant-beneficial actinobacteria associated with yam rhizosphere.

PubMed

Arunachalam Palaniyandi, Sasikumar; Yang, Seung Hwan; Damodharan, Karthiyaini; Suh, Joo-Won

2013-12-01

Actinobacteria were isolated from the rhizosphere of yam plants from agricultural fields from Yeoju, South Korea and analyzed for their genetic and plant-beneficial functional diversity. A total of 29 highly occurring actinobacterial isolates from the yam rhizosphere were screened for various plant-beneficial traits such as antimicrobial activity on fungi and bacteria; biocontrol traits such as production of siderophore, protease, chitinase, endo-cellulase, and β-glucanase. The isolates were also screened for plant growth-promoting (PGP) traits such as auxin production, phosphate solubilization, 1-aminocyclopropane-1-carboxylic acid (ACC) deaminase activity, and in vitro Arabidopsis growth promotion. 16S rDNA sequence-based phylogenetic analysis was carried out on the actinobacterial isolates to determine their genetic relatedness to known actinobacteria. BOX-PCR analysis revealed high genetic diversity among the isolates. Several isolates were identified to belong to the genus Streptomyces and a few to Kitasatospora. The actinobacterial strains exhibited high diversity in their functionality and were identified as novel and promising candidates for future development into biocontrol and PGP agents. © 2013 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

The Role of Actinobacteria in Biochar Decomposition in a Mediterranean Grassland Soil

NASA Astrophysics Data System (ADS)

Brodie, E. L.; Lim, H.; Bill, M.; Castanha, C.; Conrad, M. E.; Schmidt, M. W.; Abiven, S.; Jansson, J. K.; Torn, M. S.

2012-12-01

Biochar addition to soil has been proposed as an attractive approach for carbon sequestration, particularly in concert with bioenergy biomass production and conversion. Biochar, partially combusted organic material, is assumed to be recalcitrant in soil but studies show significant variation in residence times. The controls on biochar C stabilization are likely complex interactions among the substrate, microbial activities, and the soil chemical and physical environment. However, there is a lack of understanding regarding the impact of biochar on soil microbial populations, the organisms that may be responsible for its mineralization or the factors regulating the rate of biochar mineralization. In this study we amended a Mediterranean grassland soil (Ultic Haploxeralf) with biochar (dried chestnut pyrolized at 450°C for 5h) or non-pyrolized oak at ratios of either 1:9 or 1:2 relative to native organic carbon. Both wood and biochar resulted in a significant and dose dependent alteration of microbial community composition within 1 week relative to controls. The rate of change of microbial composition was slower for biochar than for non-pyrolized wood but in both cases Actinobacteria showed significant enrichment relative to controls. From the same grassland soils, we then isolated bacteria capable of subsisting on biochar as a sole C or N source, many of which were Actinobacteria. We selected one Streptomyces isolate and confirmed using 13C-labeled biochar that this strain was capable of biochar mineralization, and show that mineralization was accelerated in the presence of an additional carbon source. We also detected significant abiotic CO2 loss from biochar during incubations. This study demonstrates that some soil Actinobacteria can subsist on biochar as a sole C source, mineralizing it to CO2, our data also shows that priming of biochar decomposition can occur. Overall this highlights the important roles that microbial composition and resource availability may

Divergence and Phylogeny of Firmicutes from the Cuatro Ciénegas Basin, Mexico: A Window to an Ancient Ocean

PubMed Central

Moreno-Letelier, Alejandra; Olmedo-Alvarez, Gabriela; Eguiarte, Luis E.

2012-01-01

Abstract The Cuatro Ciénegas Basin (CCB) has been identified as a center of endemism for many life-forms. Nearly half the bacterial species found in the spring systems have their closest relatives in the ocean. This raises the question of whether the high diversity observed today is the product of an adaptive radiation similar to that of the Galapagos Islands or whether the bacterial groups are “survivors” of an ancient sea, which would be of interest for astrobiology. To help answer this question, we focused on Firmicutes from Cuatro Ciénegas (mainly Bacillus and Exiguobacterium). We reconstructed the phylogenetic relationships of Firmicutes with 28 housekeeping genes and dated the resulting tree using geological events as calibration points. Our results show that marine Bacillus diverged from other Bacillus strains 838 Ma, while Bacillus from Cuatro Ciénegas have divergence dates that range from 770 to 202 Ma. The members of Exiguobacterium from the CCB conform to a much younger group that diverged from the Andes strain 60 Ma and from the one in Yellowstone 183 Ma. Therefore, the diversity of Firmicutes in Cuatro Ciénegas is not the product of a recent radiation but the product of the isolation of lineages from an ancient ocean. Hence, Cuatro Ciénegas is not a Galapagos Archipelago for bacteria but is more like an astrobiological “time machine” in which bacterial lineages survived in an oligotrophic environment that may be very similar to that of the Precambrian. Key Words: Firmicutes—Cuatro Ciénegas—Precambrian—Molecular dating—Western Interior Seaway. Astrobiology 12, 674–684. PMID:22920517

Integral use of sugarcane vinasse for biomass production of actinobacteria: Potential application in soil remediation.

PubMed

Aparicio, Juan D; Benimeli, Claudia S; Almeida, César A; Polti, Marta A; Colin, Verónica L

2017-08-01

The use of living actinobacteria biomass to clean up contaminated soils is an attractive biotechnology approach. However, biomass generation from cheap feedstock is the first step to ensure process sustainability. The present work reports the ability of four actinobacteria, Streptomyces sp. M7, MC1, A5, and Amycolatopsis tucumanensis, to generate biomass from sugarcane vinasse. Optimal vinasse concentration to obtain the required biomass (more than 0.4 g L -1 ) was 20% for all strains, either grown individually or as mixed cultures. However, the biomass fraction recovered from first vinasse was discarded as it retained trace metals present in the effluent. Fractions recovered from three consecutive cycles of vinasse re-use obtained by mixing equal amounts of biomass from single cultures or produced as a mixed culture were evaluated to clean up contaminated soil with lindane and chromium. In all cases, the decrease in pesticide was about 50% after 14 d of incubation. However, chromium removal was statistically different depending on the preparation methodology of the inoculum. While the combined actinobacteria biomass recovered from their respective single cultures removed about 85% of the chromium, the mixed culture biomass removed more than 95%. At the end of the reused vinasse cycle, the mixed culture removed more than 70% of the biological oxygen demand suggesting a proportional reduction in the effluent toxicity. These results represent the first integral approach to address a problematic of multiple contaminations, concerning pesticides, heavy metals and a regionally important effluent like vinasse. Copyright © 2017 Elsevier Ltd. All rights reserved.

Insight into the effects of different cropping systems on soil bacterial community and tobacco bacterial wilt rate.

PubMed

Niu, Jiaojiao; Chao, Jin; Xiao, Yunhua; Chen, Wu; Zhang, Chao; Liu, Xueduan; Rang, Zhongwen; Yin, Huaqun; Dai, Linjian

2017-01-01

Rotation is an effective strategy to control crop disease and improve plant health. However, the effects of crop rotation on soil bacterial community composition and structure, and crop health remain unclear. In this study, using 16S rRNA gene sequencing, we explored the soil bacterial communities under four different cropping systems, continuous tobacco cropping (control group), tobacco-maize rotation, tobacco-lily rotation, and tobacco-turnip rotation. Results of detrended correspondence analysis and dissimilarity tests showed that soil bacterial community composition and structure changed significantly among the four groups, such that Acidobacteria and Actinobacteria were more abundant in the maize rotation group (16.6 and 11.5%, respectively) than in the control (8.5 and 7.1%, respectively). Compared with the control group (57.78%), maize and lily were effective rotation crops in controlling tobacco bacterial wilt (about 23.54 and 48.67%). On the other hand, tobacco bacterial wilt rate was increased in the turnip rotation (59.62%) relative to the control. Further study revealed that the abundances of several bacterial populations were directly correlated with tobacco bacterial wilt. For example, Acidobacteria and Actinobacteria were significantly negatively correlated to the tobacco bacterial wilt rate, so they may be probiotic bacteria. Canonical correspondence analysis showed that soil pH and calcium content were key factors in determining soil bacterial communities. In conclusion, our study revealed the composition and structure of bacterial communities under four different cropping systems and may unveil molecular mechanisms for the interactions between soil microorganisms and crop health. © 2016 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

Testing association between soil bacterial diversity and soil carbon storage on the Loess Plateau.

PubMed

Yang, Yang; Dou, Yanxing; An, Shaoshan

2018-06-01

Bacteria are widely distributed and play an important role in soil carbon (C) cycling. The impact of soil bacterial diversity on soil C storage has been well established, yet little is known about the underlying mechanisms and the interactions among them. Here, we examined the association between soil bacterial diversity and soil C storage in relation to vegetation restoration on the Loess Plateau. The dominant phyla among land use types (artificial forest, Af; natural shrubland, Ns; artificial grassland, Ag; natural grassland, Ng; slope cropland, Sc) were Acidobacteria, Actinobacteria, Alphaproteobacteria, and Betaproteobacteria, which transited from Acidobacteria-dominant to Actinobacteria-dominant community due to vegetation restoration. Soil C storage and the Shannon diversity index of soil bacterial community (H Bacteria ) showed the order Ns > Ng > Af > Ag > Sc, whereas no significant difference was found in Good's coverage (p > .05). Further, a strong relationship was observed between the relative abundance of dominant bacterial groups and soil C storage (p < .05). Additionally, soil bacterial diversity was closely related to soil C storage based on the structural equation model (SEM) and generalized additive models (GAMs). Specifically, soil C storage had the largest deterministic effects, explaining >70% of the variation and suggesting a strong association between soil C storage and soil bacterial diversity. Overall, we propose that further studies are necessary with a focus on the soil bacterial groups with specific functions in relation to soil C storage on the Loess Plateau. Copyright © 2018 Elsevier B.V. All rights reserved.

Next Generation Sequencing of Actinobacteria for the Discovery of Novel Natural Products

PubMed Central

Gomez-Escribano, Juan Pablo; Alt, Silke; Bibb, Mervyn J.

2016-01-01

Like many fields of the biosciences, actinomycete natural products research has been revolutionised by next-generation DNA sequencing (NGS). Hundreds of new genome sequences from actinobacteria are made public every year, many of them as a result of projects aimed at identifying new natural products and their biosynthetic pathways through genome mining. Advances in these technologies in the last five years have meant not only a reduction in the cost of whole genome sequencing, but also a substantial increase in the quality of the data, having moved from obtaining a draft genome sequence comprised of several hundred short contigs, sometimes of doubtful reliability, to the possibility of obtaining an almost complete and accurate chromosome sequence in a single contig, allowing a detailed study of gene clusters and the design of strategies for refactoring and full gene cluster synthesis. The impact that these technologies are having in the discovery and study of natural products from actinobacteria, including those from the marine environment, is only starting to be realised. In this review we provide a historical perspective of the field, analyse the strengths and limitations of the most relevant technologies, and share the insights acquired during our genome mining projects. PMID:27089350

Phylogenetic Diversity and Biological Activity of Actinobacteria Isolated from the Chukchi Shelf Marine Sediments in the Arctic Ocean

PubMed Central

Yuan, Meng; Yu, Yong; Li, Hui-Rong; Dong, Ning; Zhang, Xiao-Hua

2014-01-01

Marine environments are a rich source of Actinobacteria and have the potential to produce a wide variety of biologically active secondary metabolites. In this study, we used four selective isolation media to culture Actinobacteria from the sediments collected from the Chukchi Shelf in the Arctic Ocean. A total of 73 actinobacterial strains were isolated. Based on repetitive DNA fingerprinting analysis, we selected 30 representatives for partial characterization according to their phylogenetic diversity, antimicrobial activities and secondary-metabolite biosynthesis genes. Results from the 16S rRNA gene sequence analysis indicated that the 30 strains could be sorted into 18 phylotypes belonging to 14 different genera: Agrococcus, Arsenicicoccus, Arthrobacter, Brevibacterium, Citricoccus, Janibacter, Kocuria, Microbacterium, Microlunatus, Nocardioides, Nocardiopsis, Saccharopolyspora, Salinibacterium and Streptomyces. To our knowledge, this paper is the first report on the isolation of Microlunatus genus members from marine habitats. Of the 30 isolates, 11 strains exhibited antibacterial and/or antifungal activity, seven of which have activities against Bacillus subtilis and Candida albicans. All 30 strains have at least two biosynthetic genes, one-third of which possess more than four biosynthetic genes. This study demonstrates the significant diversity of Actinobacteria in the Chukchi Shelf sediment and their potential for producing biologically active compounds and novel material for genetic manipulation or combinatorial biosynthesis. PMID:24663116

A Walk into the LuxR Regulators of Actinobacteria: Phylogenomic Distribution and Functional Diversity

PubMed Central

Santos, Catarina Lopes; Correia-Neves, Margarida; Moradas-Ferreira, Pedro; Mendes, Marta Vaz

2012-01-01

LuxR regulators are a widely studied group of bacterial helix-turn-helix (HTH) transcription factors involved in the regulation of many genes coding for important traits at an ecological and medical level. This regulatory family is particularly known by their involvement in quorum-sensing (QS) mechanisms, i.e., in the bacterial ability to communicate through the synthesis and binding of molecular signals. However, these studies have been mainly focused on Gram-negative organisms, and the presence of LuxR regulators in the Gram-positive Actinobacteria phylum is still poorly explored. In this manuscript, the presence of LuxR regulators among Actinobacteria was assayed using a domain-based strategy. A total of 991 proteins having one LuxR domain were identified in 53 genome-sequenced actinobacterial species, of which 59% had an additional domain. In most cases (53%) this domain was REC (receiver domain), suggesting that LuxR regulators in Actinobacteria may either function as single transcription factors or as part of two-component systems. The frequency, distribution and evolutionary stability of each of these sub-families of regulators was analyzed and contextualized regarding the ecological niche occupied by each organism. The results show that the presence of extra-domains in the LuxR-regulators was likely driven by a general need to physically uncouple the signal sensing from the signal transduction. Moreover, the total frequency of LuxR regulators was shown to be dependent on genetic, metabolic and ecological variables. Finally, the functional annotation of the LuxR regulators revealed that the bacterial ecological niche has biased the specialization of these proteins. In the case of pathogens, our results suggest that LuxR regulators can be involved in virulence and are therefore promising targets for future studies in the health-related biotechnology field. PMID:23056438

Novel marine actinobacteria from emerald Andaman & Nicobar Islands: a prospective source for industrial and pharmaceutical byproducts

PubMed Central

2013-01-01

Background Andaman and Nicobar Islands situated in the eastern part of Bay of Bengal are one of the distinguished biodiversity hotspot. Even though number of studies carried out on the marine flora and fauna, the studies on actinobacteria from Andaman and Nicobar Islands are meager. The aim of the present study was to screen the actinobacteria for their characterization and identify the potential sources for industrial and pharmaceutical byproducts. Results A total of 26 actinobacterial strains were isolated from the marine sediments collected from various sites of Port Blair Bay where no collection has been characterized previously. Isolates were categorized under the genera: Saccharopolyspora, Streptomyces, Nocardiopsis, Streptoverticillium, Microtetraspora, Actinopolyspora, Actinokineospora and Dactylosporangium. Majority of the isolates were found to produce industrially important enzymes such as amylase, protease, gelatinase, lipase, DNase, cellulase, urease and phosphatase, and also exhibited substantial antibacterial activity against human pathogens. 77% of isolates exhibited significant hemolytic activity. Among 26 isolates, three strains (NIOT-VKKMA02, NIOT-VKKMA22 and NIOT-VKKMA26) were found to generate appreciable extent of surfactant, amylase, cellulase and protease enzyme. NIOT-VKKMA02 produced surfactant using kerosene as carbon source and emulsified upto E24–63.6%. Moreover, NIOT-VKKMA02, NIOT-VKKMA22 and NIOT-VKKMA26 synthesized 13.27 U/ml, 9.85 U/ml and 8.03 U/ml amylase; 7.75 U/ml, 5.01 U/ml and 2.08 U/ml of cellulase and 11.34 U/ml, 6.89 U/ml and 3.51 U/ml of protease enzyme, respectively. Conclusions High diversity of marine actinobacteria was isolated and characterized in this work including undescribed species and species not previously reported from emerald Andaman and Nicobar Islands, including Streptomyces griseus, Streptomyces venezuelae and Saccharopolyspora salina. The enhanced salt, pH and temperature tolerance of the actinobacterial

Novel marine actinobacteria from emerald Andaman & Nicobar Islands: a prospective source for industrial and pharmaceutical byproducts.

PubMed

Meena, Balakrishnan; Rajan, Lawrance Anbu; Vinithkumar, Nambali Valsalan; Kirubagaran, Ramalingam

2013-06-22

Andaman and Nicobar Islands situated in the eastern part of Bay of Bengal are one of the distinguished biodiversity hotspot. Even though number of studies carried out on the marine flora and fauna, the studies on actinobacteria from Andaman and Nicobar Islands are meager. The aim of the present study was to screen the actinobacteria for their characterization and identify the potential sources for industrial and pharmaceutical byproducts. A total of 26 actinobacterial strains were isolated from the marine sediments collected from various sites of Port Blair Bay where no collection has been characterized previously. Isolates were categorized under the genera: Saccharopolyspora, Streptomyces, Nocardiopsis, Streptoverticillium, Microtetraspora, Actinopolyspora, Actinokineospora and Dactylosporangium. Majority of the isolates were found to produce industrially important enzymes such as amylase, protease, gelatinase, lipase, DNase, cellulase, urease and phosphatase, and also exhibited substantial antibacterial activity against human pathogens. 77% of isolates exhibited significant hemolytic activity. Among 26 isolates, three strains (NIOT-VKKMA02, NIOT-VKKMA22 and NIOT-VKKMA26) were found to generate appreciable extent of surfactant, amylase, cellulase and protease enzyme. NIOT-VKKMA02 produced surfactant using kerosene as carbon source and emulsified upto E(24)-63.6%. Moreover, NIOT-VKKMA02, NIOT-VKKMA22 and NIOT-VKKMA26 synthesized 13.27 U/ml, 9.85 U/ml and 8.03 U/ml amylase; 7.75 U/ml, 5.01 U/ml and 2.08 U/ml of cellulase and 11.34 U/ml, 6.89 U/ml and 3.51 U/ml of protease enzyme, respectively. High diversity of marine actinobacteria was isolated and characterized in this work including undescribed species and species not previously reported from emerald Andaman and Nicobar Islands, including Streptomyces griseus, Streptomyces venezuelae and Saccharopolyspora salina. The enhanced salt, pH and temperature tolerance of the actinobacterial isolates along with their

Influence of land use on bacterial and archaeal diversity and community structures in three natural ecosystems and one agricultural soil.

PubMed

Lynn, Tin Mar; Liu, Qiong; Hu, Yajun; Yuan, Hongzhao; Wu, Xiaohong; Khai, Aye Aye; Wu, Jinshui; Ge, Tida

2017-07-01

Studying shifts in microbial communities under different land use can help in determining the impact of land use on microbial diversity. In this study, we analyzed four different land-use types to determine their bacterial and archaeal diversity and abundance. Three natural ecosystems, that is, wetland (WL), grassland (GL), and forest (FR) soils, and one agricultural soil, that is, tea plantation (TP) soil, were investigated to determine how land use shapes bacterial and archaeal diversity. For this purpose, molecular analyses, such as quantitative polymerase chain reaction (Q-PCR), 16S rRNA gene sequencing, and terminal restriction fragment length polymorphism (T-RFLP), were used. Soil physicochemical properties were determined, and statistical analyses were performed to identify the key factors affecting microbial diversity in these soils. Phylogenetic affiliations determined using the Ribosomal Database Project (RDP) database and T-RFLP revealed that the soils had differing bacterial diversity. WL soil was rich in only Proteobacteria, whereas GR soil was rich in Proteobacteria, followed by Actinobacteria. FR soil had higher abundance of Chloroflexi species than these soils. TP soil was rich in Actinobacteria, followed by Chloroflexi, Acidobacteria, Proteobacteria, and Firmicutes. The archaeal diversity of GL and FR soils was similar in that most of their sequences were closely related to Nitrososphaerales (Thaumarchaeota phylum). In contrast, WL soil, followed by TP soil, had greater archaeal diversity than other soils. Eight different archaeal classes were found in WL soil, and Pacearchaeota class was the richest one. The abundance of bacterial and archaeal 16S rRNA gene copies in WL and GL soils was significantly higher than that in FR and TP soils. Redundancy analysis showed that bacterial diversity was influenced by abiotic factors, e.g., total organic carbon and pH, whereas total nitrogen, pH, and cation exchange capacity (CEC) significantly affected

Soil quality and bacterial community structure: a case study from the mediterranean region

NASA Astrophysics Data System (ADS)

Anguita-Maeso, Manuel; Miralles*, Isabel; Soriano**, Miguel; Ortega, Raúl; García-Salcedo, José Antonio; Sánchez-Marañon, Manuel

2017-04-01

Bacterial communities play a central role in innumerable processes and functions of soils such as decomposition of organic residues, nutrient cycling, aggregation, and formation of humic substances. We investigated the relationships between bacterial communities, soil profiles, and quality parameters in eight benchmark soils of the Mediterranean calcareous mountain sampled on a local scale. The diversity and composition of prokaryotic community was assessed by 16S rRNA gene amplicon pyrosequencing of DNA from samples of topsoil (10 x 10 x 0.2 m). The bacterial profile content resulted in the identification of groups belonging to 16 phyla and 75 genera. Two-dimensional models using multidimensional scaling (Stress < 0.11), correspondence analysis (Inertia > 71%), and principal component analysis (Variance > 60%) showed a decrease in the abundance of acidobacteria Gp4 and Gp3 while actinobacteria flourished with increasing soil profile development (from Leptosol to Luvisol). This can be attributed to inherent changes in soil quality along pedogenesis such as pH (8.3 to 7.8), organic C (20.0 to 45.2 Mg ha-1), macropososity (0.11 to 0.32 cm3 cm-3), and water stable aggregates (365.8 to 963.4 Mg ha-1). Actinobacteria genera like Aciditerrimonas, Nocardioides, and Solirubrobacter also displayed positive correlations (r > 0.90) with the content of clay and free Ferric forms. Other factors like Re-carbonation, loss of organic matter, and soil compaction probably caused by land use and management, led to a decline in the Chao1 richness and Shannon diversity indices (3625 and 6.3) with respect to native soils (7852 and 7.4). Likewise, Firmicutes and Gemmatimonadetes were tripled and the genera of Proteobacteria and Bacteroidetes decreased. Our data indicate that bacterial community structure depends largely on the soil quality status, both inherent and managed and suggest the bacterial group composition also follows the course of soil genesis. (*) Financial support by Marie

Production of an antibiotic enterocin from a marine actinobacteria strain H1003 by metal-stress technique with enhanced enrichment using response surface methodology.

PubMed

Hassan, Syed Shamsul; Shah, Sayed Asmat Ali; Pan, Chengqian; Fu, Leilei; Cao, Xun; Shi, Yutong; Wu, Xiaodan; Wang, Kuiwu; Wu, Bin

2017-01-01

Elicitation by chemical means including heavy metals is one of a new technique for drug discoveries. In this research, the effect of heavy metals on marine actinobacteria Streptomyces sp. H-1003 for the production of enterocin, with a strong broad spectrum activity, along optimized fermented medium was firstly investigated. The optimum metal stress conditions consisted of culturing marine actinobacteria strain H-1003 with addition of cobalt ions at 2mM in optimized Gause's medium having starch at 20mg/L for 10 days at 180 revolution/min. Under these conditions, enterocin production was enhanced with a value of 5.33mg/L, which was totally absent at the normal culture of strain H-1003 and much higher than other tested metal-stress conditions. This work triumphantly announced a prodigious effect of heavy metals on marine actinobacteria with fringe benefits as a key tool of enterocin production.

Complete genome sequence of Granulicella tundricola type strain MP5ACTX9T, an Acidobacteria from tundra soil

DOE Office of Scientific and Technical Information (OSTI.GOV)

Rawat, Suman R.; Mannisto, Minna; Starovoytov, Valentin

2013-01-01

Granulicella tundricola strain MP5ACTX9T is a novel species of the genus Granulicella in subdivision 1 Acidobacteria. G. tundricola is a predominant member of soil bacterial communities, active at low temperatures and nutrient limiting conditions in Arctic alpine tundra. The organism is a cold-adapted acidophile and a versatile heterotroph that hydro-lyzes a suite of sugars and complex polysaccharides. Genome analysis revealed metabolic versatility with genes involved in metabolism and transport of carbohydrates, including gene modules encoding for the carbohydrate-active enzyme (CAZy) families for the break-down, utilization and biosynthesis of diverse structural and storage polysaccharides such as plant based carbon polymers. Themore » genome of G. tundricola strain MP5ACTX9T consists of 4,309,151 bp of a circular chromosome and five mega plasmids with a total genome con-tent of 5,503,984 bp. The genome comprises 4,705 protein-coding genes and 52 RNA genes.« less

Genetic Approach for the Fast Discovery of Phenazine Producing Bacteria

PubMed Central

Schneemann, Imke; Wiese, Jutta; Kunz, Anna Lena; Imhoff, Johannes F.

2011-01-01

A fast and efficient approach was established to identify bacteria possessing the potential to biosynthesize phenazines, which are of special interest regarding their antimicrobial activities. Sequences of phzE genes, which are part of the phenazine biosynthetic pathway, were used to design one universal primer system and to analyze the ability of bacteria to produce phenazine. Diverse bacteria from different marine habitats and belonging to six major phylogenetic lines were investigated. Bacteria exhibiting phzE gene fragments affiliated to Firmicutes, Alpha- and Gammaproteobacteria, and Actinobacteria. Thus, these are the first primers for amplifying gene fragments from Firmicutes and Alphaproteobacteria. The genetic potential for phenazine production was shown for four type strains belonging to the genera Streptomyces and Pseudomonas as well as for 13 environmental isolates from marine habitats. For the first time, the genetic ability of phenazine biosynthesis was verified by analyzing the metabolite pattern of all PCR-positive strains via HPLC-UV/MS. Phenazine production was demonstrated for the type strains known to produce endophenazines, 2-hydroxy-phenazine, phenazine-1-carboxylic acid, phenazine-1,6-dicarboxylic acid, and chlororaphin as well as for members of marine Actinobacteria. Interestingly, a number of unidentified phenazines possibly represent new phenazine structures. PMID:21673888

Effect of Bifidobacterium breve on the Intestinal Microbiota of Coeliac Children on a Gluten Free Diet: A Pilot Study.

PubMed

Quagliariello, Andrea; Aloisio, Irene; Bozzi Cionci, Nicole; Luiselli, Donata; D'Auria, Giuseppe; Martinez-Priego, Llúcia; Pérez-Villarroya, David; Langerholc, Tomaž; Primec, Maša; Mičetić-Turk, Dušanka; Di Gioia, Diana

2016-10-22

Coeliac disease (CD) is associated with alterations of the intestinal microbiota. Although several Bifidobacterium strains showed anti-inflammatory activity and prevention of toxic gliadin peptides generation in vitro, few data are available on their efficacy when administered to CD subjects. This study evaluated the effect of administration for three months of a food supplement based on two Bifidobacterium breve strains (B632 and BR03) to restore the gut microbial balance in coeliac children on a gluten free diet (GFD). Microbial DNA was extracted from faeces of 40 coeliac children before and after probiotic or placebo administration and 16 healthy children (Control group). Sequencing of the amplified V3-V4 hypervariable region of 16S rRNA gene as well as qPCR of Bidobacterium spp., Lactobacillus spp., Bacteroides fragilis group Clostridium sensu stricto and enterobacteria were performed. The comparison between CD subjects and Control group revealed an alteration in the intestinal microbial composition of coeliacs mainly characterized by a reduction of the Firmicutes/Bacteroidetes ratio, of Actinobacteria and Euryarchaeota . Regarding the effects of the probiotic, an increase of Actinobacteria was found as well as a re-establishment of the physiological Firmicutes/Bacteroidetes ratio. Therefore, a three-month administration of B. breve strains helps in restoring the healthy percentage of main microbial components.

Zinc treatment increases the titre of 'Candidatus Liberibacter asiaticus' in huanglongbing-affected citrus plants while affecting the bacterial microbiomes.

PubMed

Zhang, M Q; Guo, Y; Powell, C A; Doud, M S; Yang, C Y; Zhou, H; Duan, Y P

2016-06-01

Huanglongbing (HLB)-affected citrus often display zinc deficiency symptoms. In this study, supplemental zinc was applied to citrus to determine its effect on Candidatus Liberibacter asiaticus (Las) titre, HLB symptoms, and leaf microbiome. HLB-affected citrus were treated with various amounts of zinc. The treatments promoted Las growth and affected microbiomes in citrus leaves. Phylochip(™) -based results indicated that 5475 of over 50 000 known Operational Taxonomic Units (OTUs) in 52 phyla were detected in the midribs of HLB-affected citrus, of which Proteobacteria was the most abundant, followed by Firmicutes and Actinobacteria. In comparison, the microbiomes of zinc-treated diseased plants had overall more OTUs with higher amounts of Proteobacteria, but decreased percentages of Firmicutes and Actinobacteria. In addition, more OTUs of siderophore-producing bacteria were present. Only zinc-sensitive Staphylococcaceae had higher OTU's in the diseased plants without zinc treatments. Although HLB-affected citrus appear zinc deficient, zinc amendments increased the pathogen levels and shifted the microbiome. HLB is currently the most devastating disease of citrus worldwide. Zinc is often applied to HLB-affected citrus due to zinc deficiency symptoms. This study provided new insights into the potential effects of zinc on HLB and the microbial ecology of citrus. © 2016 The Society for Applied Microbiology.

Structure and function of methanogenic microbial communities in sediments of Amazonian lakes with different water types.

PubMed

Ji, Yang; Angel, Roey; Klose, Melanie; Claus, Peter; Marotta, Humberto; Pinho, Luana; Enrich-Prast, Alex; Conrad, Ralf

2016-12-01

Tropical lake sediments are a significant source for the greenhouse gas methane. We studied function (pathway, rate) and structure (abundance, taxonomic composition) of the microbial communities (Bacteria, Archaea) leading to methane formation together with the main physicochemical characteristics in the sediments of four clear water, six white water and three black water lakes of the Amazon River system. Concentrations of sulfate and ferric iron, pH and δ 13 C of organic carbon were usually higher, while concentrations of carbon, nitrogen and rates of CH 4 production were generally lower in white water versus clear water or black water sediments. Copy numbers of bacterial and especially archaeal ribosomal RNA genes also tended to be relatively lower in white water sediments. Hydrogenotrophic methanogenesis contributed 58 ± 16% to total CH 4 production in all systems. Network analysis identified six communities, of which four were comprised mostly of bacteria found in all sediment types, while two were mostly in clear water sediment. Terminal restriction fragment length polymorphism (T-RFLP) and pyrosequencing showed that the compositions of the communities differed between the different sediment systems, statistically related to the particular physicochemical conditions and to CH 4 production rates. Among the archaea, clear water, white water, and black water sediments contained relatively more Methanomicrobiales, Methanosarcinaceae and Methanocellales, respectively, while Methanosaetaceae were common in all systems. Proteobacteria, Deltaproteobacteria (Myxococcales, Syntrophobacterales, sulfate reducers) in particular, Acidobacteria and Firmicutes were the most abundant bacterial phyla in all sediment systems. Among the other important bacterial phyla, clear water sediments contained relatively more Alphaproteobacteria and Planctomycetes, whereas white water sediments contained relatively more Betaproteobacteria, Firmicutes, Actinobacteria, and Chloroflexi

Culture-dependent and culture-independent diversity of Actinobacteria associated with the marine sponge Hymeniacidon perleve from the South China Sea.

PubMed

Sun, Wei; Dai, Shikun; Jiang, Shumei; Wang, Guanghua; Liu, Guohui; Wu, Houbo; Li, Xiang

2010-06-01

In this report, the diversity of Actinobacteria associated with the marine sponge Hymeniacidon perleve collected from a remote island of the South China Sea was investigated employing classical cultivation and characterization, 16S rDNA library construction, 16S rDNA-restriction fragment length polymorphism (rDNA-RFLP) and phylogenetic analysis. A total of 184 strains were isolated using seven different media and 24 isolates were selected according to their morphological characteristics for phylogenetic analysis on the basis of their 16S rRNA gene sequences. Results showed that the 24 isolates were assigned to six genera including Salinispora, Gordonia, Mycobacterium, Nocardia, Rhodococcus and Streptomyces. This is the first report that Salinispora is present in a marine sponge from the South China Sea. Subsequently, 26 rDNA clones were selected from 191 clones in an Actinobacteria-specific 16S rDNA library of the H. perleve sample, using the RFLP technique for sequencing and phylogenetic analysis. In total, 26 phylotypes were clustered in eight known genera of Actinobacteria including Mycobacterium, Amycolatopsis, Arthrobacter, Brevibacterium, Microlunatus, Nocardioides, Pseudonocardia and Streptomyces. This study contributes to our understanding of actinobacterial diversity in the marine sponge H. perleve from the South China Sea.

Variability of Prokaryotic Community Structure in a Drinking Water Reservoir (Marathonas, Greece)

PubMed Central

Lymperopoulou, Despoina S.; Kormas, Konstantinos Ar.; Karagouni, Amalia D.

2012-01-01

The structure of the Bacteria and Archaea community in a large drinking water reservoir (Marathonas, Greece; MR) was investigated in October 2007 and September 2008, using 16S rRNA gene clone libraries. The bacterial communities were more diverse than archaeal communities (Shannon diversity index H′ 0.81–3.28 and 1.36–1.77, respectively). The overall bacterial community composition was comparable to bacterioplankton community described in other freshwater habitats. Within the Bacteria, Betaproteobacteria dominated, while representatives of Alpha-, Gamma- and Deltaproteobacteria also occurred. Other important phyla were Actinobacteria and Bacteroidetes, while representatives of Acidobacteria, Cyanobacteria, Chloroflexi, Planctomycetes and Verrucomicrobia were also retrieved. Several phylotypes in Alpha- and Betaproteobacteria and Bacteroidetes were related to bacteria capable of cyanotoxin degradation and with aromatic compounds/iron oxidizers or polymer degraders. Euryarchaeota dominated (60.5%) the Archaea community mostly with phylotypes related to Methanobacteriales and Methanosarcinales. Among the Thaumarchaeota, the two most abundant phylotypes were affiliated (97% similarity) with the only cultivated mesophilic thaumarchaeote of marine origin, Nitrosopumilus maritimus. Temporal and spatial comparison of the prokaryotic community structure revealed that three of the most abundant prokaryotic phylotypes, belonging to Actinobacteria, were recovered from all sites both years, suggesting that these Actinobacteria could be important key players in MR ecosystem functioning. PMID:21971081

Endophytic Actinobacteria from the Brazilian Medicinal Plant Lychnophora ericoides Mart. and the Biological Potential of Their Secondary Metabolites.

PubMed

Conti, Raphael; Chagas, Fernanda Oliveira; Caraballo-Rodriguez, Andrés Mauricio; Melo, Weilan Gomes da Paixão; do Nascimento, Andréa Mendes; Cavalcanti, Bruno Coêlho; de Moraes, Manoel Odorico; Pessoa, Cláudia; Costa-Lotufo, Letícia Veras; Krogh, Renata; Andricopulo, Adriano Defini; Lopes, Norberto Peporine; Pupo, Mônica Tallarico

2016-06-01

Endophytic actinobacteria from the Brazilian medicinal plant Lychnophora ericoides were isolated for the first time, and the biological potential of their secondary metabolites was evaluated. A phylogenic analysis of isolated actinobacteria was accomplished with 16S rRNA gene sequencing, and the predominance of the genus Streptomyces was observed. All strains were cultured on solid rice medium, and ethanol extracts were evaluated with antimicrobial and cytotoxic assays against cancer cell lines. As a result, 92% of the extracts showed a high or moderate activity against at least one pathogenic microbial strain or cancer cell line. Based on the biological and chemical analyses of crude extracts, three endophytic strains were selected for further investigation of their chemical profiles. Sixteen compounds were isolated, and 3-hydroxy-4-methoxybenzamide (9) and 2,3-dihydro-2,2-dimethyl-4(1H)-quinazolinone (15) are reported as natural products for the first time in this study. The biological activity of the pure compounds was also assessed. Compound 15 displayed potent cytotoxic activity against all four tested cancer cell lines. Nocardamine (2) was only moderately active against two cancer cell lines but showed strong activity against Trypanosoma cruzi. Our results show that endophytic actinobacteria from L. ericoides are a promising source of bioactive compounds. © 2016 Verlag Helvetica Chimica Acta AG, Zürich.

Isolation and screening of proangiogenic and antiangiogenic metabolites producing rare actinobacteria from soil.

PubMed

Azarakhsh, Y; Mohammadipanah, F; Nassiri, S M; Siavashi, V; Hamedi, J

2017-06-01

Angiogenesis is a physiological process that has important impacts on the pathology and healing of various diseases, and its induction or inhibition by bioactive actinobacterial metabolites can help the treatment of some diseases. In this study, the effects of actinobacterial extract in the process of angiogenesis have been explored. In this research, proangiogenic and antiangiogenic metabolites producing actinobacteria were isolated from soil samples and their fermentation broth were extracted and after evaluation of their toxicity by MTT assay, antiangiogenic and proangiogenic activities were screened against human umbilical vein endothelial cells (HUVECs) by in vitro tube formation and migration assay. Isolated strains were identified through molecular techniques. The results showed that Nocardiopsis arvandica UTMC 103 and Nonomuraea sp. UTMC 2180 extracts had a high potential of anti-angiogenic activity on HUVECs. For the first time proangiogenic potency of a rare actinobacterium, Kribbella sp. UTMC 522, was reported, and N. arvandica UTMC 103 and Nonomuraea sp. UTMC 2180 extracts inhibits the proliferation, migration and angiogenesis activity of HUVECs with reasonable potency. Metabolites of the introduced rare actinobacteria are potent proangiogenic and angiogenic inhibitors. Identification of angiogenic-antiangiogenic mechanisms and purification of the extracts would be useful in therapeutic angiogenesis. © 2017 The Society for Applied Microbiology.

Characterization of Trapped Lignin-Degrading Microbes in Tropical Forest Soil

DOE Office of Scientific and Technical Information (OSTI.GOV)

DeAngelis, Kristen M.; Allgaier, Martin; Chavarria, Yaucin

2011-04-29

Lignin is often the most difficult portion of plant biomass to degrade, with fungi generally thought to dominate during late stage decomposition. Lignin in feedstock plant material represents a barrier to more efficient plant biomass conversion and can also hinder enzymatic access to cellulose, which is critical for biofuels production. Tropical rain forest soils in Puerto Rico are characterized by frequent anoxic conditions and fluctuating redox, suggesting the presence of lignin-degrading organisms and mechanisms that are different from known fungal decomposers and oxygen-dependent enzyme activities. We explored microbial lignin-degraders by burying bio-traps containing lignin-amended and unamended biosep beads in themore » soil for 1, 4, 13 and 30 weeks. At each time point, phenol oxidase and peroxidase enzyme activity was found to be elevated in the lignin-amended versus the unamended beads, while cellulolytic enzyme activities were significantly depressed in lignin-amended beads. Quantitative PCR of bacterial communities showed more bacterial colonization in the lignin-amended compared to the unamended beads after one and four weeks, suggesting that the lignin supported increased bacterial abundance. The microbial community was analyzed by small subunit 16S ribosomal RNA genes using microarray (PhyloChip) and by high-throughput amplicon pyrosequencing based on universal primers targeting bacterial, archaeal, and eukaryotic communities. Community trends were significantly affected by time and the presence of lignin on the beads. Lignin-amended beads have higher relative abundances of representatives from the phyla Actinobacteria, Firmicutes, Acidobacteria and Proteobacteria compared to unamended beads. This study suggests that in low and fluctuating redox soils, bacteria could play a role in anaerobic lignin decomposition.« less

Characterization of trapped lignin-degrading microbes in tropical forest soil

DOE Office of Scientific and Technical Information (OSTI.GOV)

DeAngelis, K.M.; Allgaier, M.; Chavarria, Y.

2011-03-01

Lignin is often the most difficult portion of plant biomass to degrade, with fungi generally thought to dominate during late stage decomposition. Lignin in feedstock plant material represents a barrier to more efficient plant biomass conversion and can also hinder enzymatic access to cellulose, which is critical for biofuels production. Tropical rain forest soils in Puerto Rico are characterized by frequent anoxic conditions and fluctuating redox, suggesting the presence of lignin-degrading organisms and mechanisms that are different from known fungal decomposers and oxygen-dependent enzyme activities. We explored microbial lignin-degraders by burying bio-traps containing lignin-amended and unamended biosep beads in themore » soil for 1, 4, 13 and 30 weeks. At each time point, phenol oxidase and peroxidase enzyme activity was found to be elevated in the lignin-amended versus the unamended beads, while cellulolytic enzyme activities were significantly depressed in lignin-amended beads. Quantitative PCR of bacterial communities showed more bacterial colonization in the lignin-amended compared to the unamended beads after one and four weeks, suggesting that the lignin supported increased bacterial abundance. The microbial community was analyzed by small subunit 16S ribosomal RNA genes using microarray (PhyloChip) and by high-throughput amplicon pyrosequencing based on universal primers targeting bacterial, archaeal, and eukaryotic communities. Community trends were significantly affected by time and the presence of lignin on the beads. Lignin-amended beads have higher relative abundances of representatives from the phyla Actinobacteria, Firmicutes, Acidobacteria and Proteobacteria compared to unamended beads. This study suggests that in low and fluctuating redox soils, bacteria could play a role in anaerobic lignin decomposition.« less

Characterization of Trapped Lignin-Degrading Microbes in Tropical Forest Soil

DOE Office of Scientific and Technical Information (OSTI.GOV)

DeAngelis, Kristen; Allgaier, Martin; Chavarria, Yaucin

2011-07-14

Lignin is often the most difficult portion of plant biomass to degrade, with fungi generally thought to dominate during late stage decomposition. Lignin in feedstock plant material represents a barrier to more efficient plant biomass conversion and can also hinder enzymatic access to cellulose, which is critical for biofuels production. Tropical rain forest soils in Puerto Rico are characterized by frequent anoxic conditions and fluctuating redox, suggesting the presence of lignin-degrading organisms and mechanisms that are different from known fungal decomposers and oxygen-dependent enzyme activities. We explored microbial lignin-degraders by burying bio-traps containing lignin-amended and unamended biosep beads in themore » soil for 1, 4, 13 and 30 weeks. At each time point, phenol oxidase and peroxidase enzyme activity was found to be elevated in the lignin-amended versus the unamended beads, while cellulolytic enzyme activities were significantly depressed in lignin-amended beads. Quantitative PCR of bacterial communities showed more bacterial colonization in the lignin-amended compared to the unamended beads after one and four weeks, suggesting that the lignin supported increased bacterial abundance. The microbial community was analyzed by small subunit 16S ribosomal RNA genes using microarray (PhyloChip) and by high-throughput amplicon pyrosequencing based on universal primers targeting bacterial, archaeal, and eukaryotic communities. Community trends were significantly affected by time and the presence of lignin on the beads. Lignin-amended beads have higher relative abundances of representatives from the phyla Actinobacteria, Firmicutes, Acidobacteria and Proteobacteria compared to unamended beads. This study suggests that in low and fluctuating redox soils, bacteria could play a role in anaerobic lignin decomposition.« less

Microbial diversity in hummock and hollow soils of three wetlands on the Qinghai-Tibetan Plateau revealed by 16S rRNA pyrosequencing.

PubMed

Deng, Yongcui; Cui, Xiaoyong; Hernández, Marcela; Dumont, Marc G

2014-01-01

The wetlands of the Qinghai-Tibetan Plateau are believed to play an important role in global nutrient cycling, but the composition and diversity of microorganisms in this ecosystem are poorly characterized. An understanding of the effects of geography and microtopography on microbial populations will provide clues to the underlying mechanisms that structure microbial communities. In this study, we used pyrosequencing-based analysis of 16S rRNA gene sequences to assess and compare the composition of soil microbial communities present in hummock and hollow soils from three wetlands (Dangxiong, Hongyuan and Maduo) on the Qinghai-Tibetan Plateau, the world's highest plateau. A total of 36 bacterial phyla were detected. Proteobacteria (34.5% average relative abundance), Actinobacteria (17.3%) and Bacteroidetes (11%) had the highest relative abundances across all sites. Chloroflexi, Acidobacteria, Verrucomicrobia, Firmicutes, and Planctomycetes were also relatively abundant (1-10%). In addition, archaeal sequences belonging to Euryarchaea, Crenarchaea and Thaumarchaea were detected. Alphaproteobacteria sequences, especially of the order Rhodospirillales, were significantly more abundant in Maduo than Hongyuan and Dangxiong wetlands. Compared with Hongyuan soils, Dangxiong and Maduo had significantly higher relative abundances of Gammaproteobacteria sequences (mainly order Xanthomonadales). Hongyuan wetland had a relatively high abundance of methanogens (mainly genera Methanobacterium, Methanosarcina and Methanosaeta) and methanotrophs (mainly Methylocystis) compared with the other two wetlands. Principal coordinate analysis (PCoA) indicated that the microbial community structure differed between locations and microtopographies and canonical correspondence analysis indicated an association between microbial community structure and soil properties or geography. These insights into the microbial community structure and the main controlling factors in wetlands of the Qinghai

Long-Term Nitrogen Amendment Alters the Diversity and Assemblage of Soil Bacterial Communities in Tallgrass Prairie

PubMed Central

Todd, Timothy C.; Blair, John M.; Herman, Michael A.

2013-01-01

Anthropogenic changes are altering the environmental conditions and the biota of ecosystems worldwide. In many temperate grasslands, such as North American tallgrass prairie, these changes include alteration in historically important disturbance regimes (e.g., frequency of fires) and enhanced availability of potentially limiting nutrients, particularly nitrogen. Such anthropogenically-driven changes in the environment are known to elicit substantial changes in plant and consumer communities aboveground, but much less is known about their effects on soil microbial communities. Due to the high diversity of soil microbes and methodological challenges associated with assessing microbial community composition, relatively few studies have addressed specific taxonomic changes underlying microbial community-level responses to different fire regimes or nutrient amendments in tallgrass prairie. We used deep sequencing of the V3 region of the 16S rRNA gene to explore the effects of contrasting fire regimes and nutrient enrichment on soil bacterial communities in a long-term (20 yrs) experiment in native tallgrass prairie in the eastern Central Plains. We focused on responses to nutrient amendments coupled with two extreme fire regimes (annual prescribed spring burning and complete fire exclusion). The dominant bacterial phyla identified were Proteobacteria, Verrucomicrobia, Bacteriodetes, Acidobacteria, Firmicutes, and Actinobacteria and made up 80% of all taxa quantified. Chronic nitrogen enrichment significantly impacted bacterial community diversity and community structure varied according to nitrogen treatment, but not phosphorus enrichment or fire regime. We also found significant responses of individual bacterial groups including Nitrospira and Gammaproteobacteria to long-term nitrogen enrichment. Our results show that soil nitrogen enrichment can significantly alter bacterial community diversity, structure, and individual taxa abundance, which have important

Bacterial diversity in the rhizosphere of cucumbers grown in soils covering a wide range of cucumber cropping histories and environmental conditions.

PubMed

Tian, Yongqiang; Gao, Lihong

2014-11-01

Rhizosphere microorganisms in soils are important for plant growth. However, the importance of rhizosphere microorganisms is still underestimated since many microorganisms associated with plant roots cannot be cultured and since the microbial diversity in the rhizosphere can be influenced by several factors, such as the cropping history, biogeography, and agricultural practice. Here, we characterized the rhizosphere bacterial diversity of cucumber plants grown in soils covering a wide range of cucumber cropping histories and environmental conditions by using pyrosequencing of bacterial 16S rRNA genes. We also tested the effects of compost addition and/or bacterial inoculation on the bacterial diversity in the rhizosphere. We identified an average of approximately 8,883 reads per sample, corresponding to around 4,993 molecular operational taxonomic units per sample. The Proteobacteria was the most abundant phylum in almost all soils. The abundances of the phyla Bacteroidetes, Actinobacteria, Firmicutes, Acidobacteria, and Verrucomicrobia varied among the samples, and together with Proteobacteria, these phyla were the six most abundant phyla in almost all analyzed samples. Analyzing all the sample libraries together, the predominant genera found were Flavobacterium, Ohtaekwangia, Opitutus, Gp6, Steroidobacter, and Acidovorax. Overall, compost and microbial amendments increased shoot biomass when compared to untreated soils. However, compost addition decreased the bacterial α-diversity in most soils (but for three soils compost increased diversity), and no statistical effect of microbial amendment on the bacterial α-diversity was found. Moreover, soil amendments did not significantly influence the bacterial β-diversity. Soil organic content appeared more important than compost and microbial amendments in shaping the structure of bacterial communities in the rhizosphere of cucumber.

Abiotic Factors Shape Microbial Diversity in Sonoran Desert Soils

PubMed Central

Fitak, Robert R.; Munguia-Vega, Adrian; Racolta, Adriana; Martinson, Vincent G.; Dontsova, Katerina

2012-01-01

High-throughput, culture-independent surveys of bacterial and archaeal communities in soil have illuminated the importance of both edaphic and biotic influences on microbial diversity, yet few studies compare the relative importance of these factors. Here, we employ multiplexed pyrosequencing of the 16S rRNA gene to examine soil- and cactus-associated rhizosphere microbial communities of the Sonoran Desert and the artificial desert biome of the Biosphere2 research facility. The results of our replicate sampling approach show that microbial communities are shaped primarily by soil characteristics associated with geographic locations, while rhizosphere associations are secondary factors. We found little difference between rhizosphere communities of the ecologically similar saguaro (Carnegiea gigantea) and cardón (Pachycereus pringlei) cacti. Both rhizosphere and soil communities were dominated by the disproportionately abundant Crenarchaeota class Thermoprotei, which comprised 18.7% of 183,320 total pyrosequencing reads from a comparatively small number (1,337 or 3.7%) of the 36,162 total operational taxonomic units (OTUs). OTUs common to both soil and rhizosphere samples comprised the bulk of raw sequence reads, suggesting that the shared community of soil and rhizosphere microbes constitute common and abundant taxa, particularly in the bacterial phyla Proteobacteria, Actinobacteria, Planctomycetes, Firmicutes, Bacteroidetes, Chloroflexi, and Acidobacteria. The vast majority of OTUs, however, were rare and unique to either soil or rhizosphere communities and differed among locations dozens of kilometers apart. Several soil properties, particularly soil pH and carbon content, were significantly correlated with community diversity measurements. Our results highlight the importance of culture-independent approaches in surveying microbial communities of extreme environments. PMID:22885757

Changes in Bacterial and Fungal Communities across Compost Recipes, Preparation Methods, and Composting Times

PubMed Central

Neher, Deborah A.; Weicht, Thomas R.; Bates, Scott T.; Leff, Jonathan W.; Fierer, Noah

2013-01-01

Compost production is a critical component of organic waste handling, and compost applications to soil are increasingly important to crop production. However, we know surprisingly little about the microbial communities involved in the composting process and the factors shaping compost microbial dynamics. Here, we used high-throughput sequencing approaches to assess the diversity and composition of both bacterial and fungal communities in compost produced at a commercial-scale. Bacterial and fungal communities responded to both compost recipe and composting method. Specifically, bacterial communities in manure and hay recipes contained greater relative abundances of Firmicutes than hardwood recipes with hay recipes containing relatively more Actinobacteria and Gemmatimonadetes. In contrast, hardwood recipes contained a large relative abundance of Acidobacteria and Chloroflexi. Fungal communities of compost from a mixture of dairy manure and silage-based bedding were distinguished by a greater relative abundance of Pezizomycetes and Microascales. Hay recipes uniquely contained abundant Epicoccum, Thermomyces, Eurotium, Arthrobotrys, and Myriococcum. Hardwood recipes contained relatively abundant Sordariomycetes. Holding recipe constant, there were significantly different bacterial and fungal communities when the composting process was managed by windrow, aerated static pile, or vermicompost. Temporal dynamics of the composting process followed known patterns of degradative succession in herbivore manure. The initial community was dominated by Phycomycetes, followed by Ascomycota and finally Basidiomycota. Zygomycota were associated more with manure-silage and hay than hardwood composts. Most commercial composters focus on the thermophilic phase as an economic means to insure sanitation of compost from pathogens. However, the community succeeding the thermophilic phase begs further investigation to determine how the microbial dynamics observed here can be best managed

Changes in bacterial and fungal communities across compost recipes, preparation methods, and composting times.

PubMed

Neher, Deborah A; Weicht, Thomas R; Bates, Scott T; Leff, Jonathan W; Fierer, Noah

2013-01-01

Compost production is a critical component of organic waste handling, and compost applications to soil are increasingly important to crop production. However, we know surprisingly little about the microbial communities involved in the composting process and the factors shaping compost microbial dynamics. Here, we used high-throughput sequencing approaches to assess the diversity and composition of both bacterial and fungal communities in compost produced at a commercial-scale. Bacterial and fungal communities responded to both compost recipe and composting method. Specifically, bacterial communities in manure and hay recipes contained greater relative abundances of Firmicutes than hardwood recipes with hay recipes containing relatively more Actinobacteria and Gemmatimonadetes. In contrast, hardwood recipes contained a large relative abundance of Acidobacteria and Chloroflexi. Fungal communities of compost from a mixture of dairy manure and silage-based bedding were distinguished by a greater relative abundance of Pezizomycetes and Microascales. Hay recipes uniquely contained abundant Epicoccum, Thermomyces, Eurotium, Arthrobotrys, and Myriococcum. Hardwood recipes contained relatively abundant Sordariomycetes. Holding recipe constant, there were significantly different bacterial and fungal communities when the composting process was managed by windrow, aerated static pile, or vermicompost. Temporal dynamics of the composting process followed known patterns of degradative succession in herbivore manure. The initial community was dominated by Phycomycetes, followed by Ascomycota and finally Basidiomycota. Zygomycota were associated more with manure-silage and hay than hardwood composts. Most commercial composters focus on the thermophilic phase as an economic means to insure sanitation of compost from pathogens. However, the community succeeding the thermophilic phase begs further investigation to determine how the microbial dynamics observed here can be best managed

Characterization of Trapped Lignin-Degrading Microbes in Tropical Forest Soil

PubMed Central

DeAngelis, Kristen M.; Allgaier, Martin; Chavarria, Yaucin; Fortney, Julian L.; Hugenholtz, Phillip; Simmons, Blake; Sublette, Kerry; Silver, Whendee L.; Hazen, Terry C.

2011-01-01

Lignin is often the most difficult portion of plant biomass to degrade, with fungi generally thought to dominate during late stage decomposition. Lignin in feedstock plant material represents a barrier to more efficient plant biomass conversion and can also hinder enzymatic access to cellulose, which is critical for biofuels production. Tropical rain forest soils in Puerto Rico are characterized by frequent anoxic conditions and fluctuating redox, suggesting the presence of lignin-degrading organisms and mechanisms that are different from known fungal decomposers and oxygen-dependent enzyme activities. We explored microbial lignin-degraders by burying bio-traps containing lignin-amended and unamended biosep beads in the soil for 1, 4, 13 and 30 weeks. At each time point, phenol oxidase and peroxidase enzyme activity was found to be elevated in the lignin-amended versus the unamended beads, while cellulolytic enzyme activities were significantly depressed in lignin-amended beads. Quantitative PCR of bacterial communities showed more bacterial colonization in the lignin-amended compared to the unamended beads after one and four weeks, suggesting that the lignin supported increased bacterial abundance. The microbial community was analyzed by small subunit 16S ribosomal RNA genes using microarray (PhyloChip) and by high-throughput amplicon pyrosequencing based on universal primers targeting bacterial, archaeal, and eukaryotic communities. Community trends were significantly affected by time and the presence of lignin on the beads. Lignin-amended beads have higher relative abundances of representatives from the phyla Actinobacteria, Firmicutes, Acidobacteria and Proteobacteria compared to unamended beads. This study suggests that in low and fluctuating redox soils, bacteria could play a role in anaerobic lignin decomposition. PMID:21559391

The phylogenetic composition and structure of soil microbial communities shifts in response to elevated carbon dioxide.

PubMed

He, Zhili; Piceno, Yvette; Deng, Ye; Xu, Meiying; Lu, Zhenmei; Desantis, Todd; Andersen, Gary; Hobbie, Sarah E; Reich, Peter B; Zhou, Jizhong

2012-02-01

One of the major factors associated with global change is the ever-increasing concentration of atmospheric CO(2). Although the stimulating effects of elevated CO(2) (eCO(2)) on plant growth and primary productivity have been established, its impacts on the diversity and function of soil microbial communities are poorly understood. In this study, phylogenetic microarrays (PhyloChip) were used to comprehensively survey the richness, composition and structure of soil microbial communities in a grassland experiment subjected to two CO(2) conditions (ambient, 368 p.p.m., versus elevated, 560 p.p.m.) for 10 years. The richness based on the detected number of operational taxonomic units (OTUs) significantly decreased under eCO(2). PhyloChip detected 2269 OTUs derived from 45 phyla (including two from Archaea), 55 classes, 99 orders, 164 families and 190 subfamilies. Also, the signal intensity of five phyla (Crenarchaeota, Chloroflexi, OP10, OP9/JS1, Verrucomicrobia) significantly decreased at eCO(2), and such significant effects of eCO(2) on microbial composition were also observed at the class or lower taxonomic levels for most abundant phyla, such as Proteobacteria, Firmicutes, Actinobacteria, Bacteroidetes and Acidobacteria, suggesting a shift in microbial community composition at eCO(2). Additionally, statistical analyses showed that the overall taxonomic structure of soil microbial communities was altered at eCO(2). Mantel tests indicated that such changes in species richness, composition and structure of soil microbial communities were closely correlated with soil and plant properties. This study provides insights into our understanding of shifts in the richness, composition and structure of soil microbial communities under eCO(2) and environmental factors shaping the microbial community structure.

Correction to: Microbial diversity of saline environments: searching for cytotoxic activities.

PubMed

Díaz-Cárdenas, Carolina; Cantillo, Angela; Rojas, Laura Yinneth; Sandoval, Tito; Fiorentino, Susana; Robles, Jorge; Ramos, Freddy A; Zambrano, María Mercedes; Baena, Sandra

2018-03-09

The original version of this article (Diaz-Cardenas et al. 2017) unfortunately contained a mistake in Fig. 1. The pie chart of Fig. 1 should explain the distribution of the relative abundance of the Bacteria and Archaea strains isolated at Zipaquirá salt mine: Proteobacteria 39%; Actinobacteria 9%, Bacteroidetes 1%, Archaea 3% and Firmicutes 48% instead of NOMBRE DE CATEGORIA [PORCENTAJE]. The corrected Fig. 1 and caption are given below.

Novel Firmicutes Group Implicated in the Dechlorination of Two Chlorinated Xanthones, Analogues of Natural Organochlorines

PubMed Central

Krzmarzick, Mark J.; Miller, Hanna R.; Yan, Tao

2014-01-01

Although the abundance and diversity of natural organochlorines are well established, much is still unknown about the degradation of these compounds. Triplicate microcosms were used to determine whether, and which, bacterial communities could dechlorinate two chlorinated xanthones (2,7-dichloroxanthone and 5,7-dichloro-1,3-dihydroxylxanthone), analogues of a diverse class of natural organochlorines. According to quantitative-PCR (qPCR) results, several known dechlorinating genera were either not present or not enriched during dechlorination of the xanthones. Denaturing gradient gel electrophoresis, however, indicated that several Firmicutes were enriched in the dechlorinating cultures compared to triplicate controls amended with nonchlorinated xanthones. One such group, herein referred to as the Gopher group, was further studied with a novel qPCR method that confirmed enrichment of Gopher group 16S rRNA genes in the dechlorinating cultures. The enrichment of the Gopher group was again tested with two new sets of triplicate microcosms. Enrichment was observed during chlorinated xanthone dechlorination in one set of these triplicate microcosms. In the other set, two microcosms showed clear enrichment while a third did not. The Gopher group is a previously unidentified group of Firmicutes, distinct from but related to the Dehalobacter and Desulfitobacterium genera; this group also contains clones from at least four unique cultures capable of dechlorinating anthropogenic organochlorines that have been previously described in the literature. This study suggests that natural chlorinated xanthones may be effective biostimulants to enhance the remediation of pollutants and highlights the idea that novel genera of dechlorinators likely exist and may be active in bioremediation and the natural cycling of chlorine. PMID:24296507

Characterization and phylogenetic affiliation of Actinobacteria from tropical soils with potential uses for agro-industrial processes.

PubMed

Dornelas, J C M; Figueiredo, J E F; de Abreu, C S; Lana, U G P; Oliveira, C A; Marriel, I E

2017-08-31

Secondary metabolites produced by Actinobacteria of tropical soils represent a largely understudied source of novel molecules with relevant application in medicine, pharmaceutical and food industries, agriculture, and environmental bioremediation. The present study aimed to characterize sixty-nine Actinobacteria isolated from compost and tropical soils using morphological, biochemical, and molecular methods. All the isolates showed high variation for morphological traits considering the color of pigments of the aerial and vegetative mycelium and spore chain morphology. The enzymatic activity of amylase, cellulase, and lipase was highly variable. The amylase activity was detected in 53 (76.81%) isolates. Eighteen isolates showed enzymatic index (EI) > 4.0, and the isolates ACJ 45 (Streptomyces curacoi) and ACSL 6 (S. hygroscopicus) showed the highest EI values (6.44 and 6.42, respectively). The cellulase activity varied significantly (P ≤ 0.05) among the isolates. Twenty-nine isolates (42.02%) showed high cellulase activity, and the isolates ACJ 48 (S. chiangmaiensis) and ACJ 53 (S. cyslabdanicus) showed the highest EI values (6.56 for both isolates). The lipase activity varied statistically (P ≤ 0.05) with fourteen isolates (20.29%) considered good lipase producers (EI > 2.0). The isolate ACSL 6 (S. hygroscopicus) showed the highest EI value of 2.60. Molecular analysis of partial 16S rRNA gene sequencing revealed the existence of 49 species, being 38 species with only one representative member and 11 species represented by one or more strains. All species belonged to three genera, namely Streptomyces (82.61%), Amycolatopsis (7.25%), and Kitasatospora (10.14%). The present results showed the high biotechnological potential of different Actinobacteria from tropical soils.

Phylogenetic diversity and biological activity of culturable Actinobacteria isolated from freshwater fish gut microbiota.

PubMed

Jami, Mansooreh; Ghanbari, Mahdi; Kneifel, Wolfgang; Domig, Konrad J

2015-06-01

The diversity of Actinobacteria isolated from the gut microbiota of two freshwater fish species namely Schizothorax zarudnyi and Schizocypris altidorsalis was investigated employing classical cultivation techniques, repetitive sequence-based PCR (rep-PCR), partial and full 16S rDNA sequencing followed by phylogenetic analysis. A total of 277 isolates were cultured by applying three different agar media. Based on rep-PCR profile analysis a subset of 33 strains was selected for further phylogenetic investigations, antimicrobial activity testing and diversity analysis of secondary-metabolite biosynthetic genes. The identification based on 16S rRNA gene sequencing revealed that the isolates belong to eight genera distributed among six families. At the family level, 72% of the 277 isolates belong to the family Streptomycetaceae. Among the non-streptomycetes group, the most dominant group could be allocated to the family of Pseudonocardiaceae followed by the members of Micromonosporaceae. Phylogenetic analysis clearly showed that many of the isolates in the genera Streptomyces, Saccharomonospora, Micromonospora, Nocardiopsis, Arthrobacter, Kocuria, Microbacterium and Agromyces formed a single and distinct cluster with the type strains. Notably, there is no report so far about the occurrence of these Actinobacteria in the microbiota of freshwater fish. Of the 33 isolates, all the strains exhibited antibacterial activity against a set of tested human and fish pathogenic bacteria. Then, to study their associated potential capacity to synthesize diverse bioactive natural products, diversity of genes associated with secondary-metabolite biosynthesis including PKS I, PKS II, NRPS, the enzyme PhzE of the phenazine pathways, the enzyme dTGD of 6-deoxyhexoses glycosylation pathway, the enzyme Halo of halogenation pathway and the enzyme CYP in polyene polyketide biosynthesis were investigated among the isolates. All the strains possess at least two types of the investigated

Microbiome of Yermic Regosol in southern Kazakhstan

NASA Astrophysics Data System (ADS)

Kutovaya, Olga; Lebedeva, Marina; Tkhakakhova, Azida

2014-05-01

Biological activity is of utmost importance for the genesis of extremely arid desert soils. The soil surface in arid regions is often covered by biofilms representing a complex biocenosis of algae, bacteria, micromycetes, and, sometimes, mosses or lichens. Biofilms of extremely arid soils form a significant part of the living matter in the desert ecosystems and play the central role in their dynamics. Study of the genetic material recovered directly from the soil samples is the main approach in soil metagenomics. Modern sequencing methods were used to describe the diversity of the microorganisms in soil samples. For the first time, such data were obtained for the extremely arid desert soil (Yermic Regosol) in southern Kazakhstan (flat alluvial plain; 43° 42'53.2" N; 79°25'29.1" E; 615 m asl). Taxonomic identification of nucleotide sequences and comparative analysis of microbial communities were performed using VAMPS. The classification of the sequences was performed using RDP. As the primers used were based on the sequences of 16S-rRNA gene of bacteria and archaea, we could analyze the prokaryotic community. Along with bacteria and archaea with established systematic position, all soil samples contained unidentified sequences (5.2-5.3%). Bacteria predominated at the domain level (65.9-74.9%), although their portion was much lower in comparison with that in less arid soils, where it reached 94-100%. Archaea were present as minor components (0.3-0.5%). Dominant groups of bacteria were represented by Proteobacteria (43.9-50.8%), Actinobacteria (9.5-10%), Firmicutes (0.8-2.4%), Verrucomicrobia (1.1-3%), Acidobacteria (1.1-2%), Bacteroidetes (1.2-1.4%). The portion of other phyla was less than 1%. Thus, bacterial phyla Proteobacteria, Actinobacteria and Acidobacteria constitute the core component of the microbiome. Archaea are represented by phylum Crenarchaeota. A key feature of the extremely arid soils is the presence of large numbers (24.7-33.6%) of cyanobacteria

Cultivation of Hard-To-Culture Subsurface Mercury-Resistant Bacteria and Discovery of New merA Gene Sequences▿

PubMed Central

Rasmussen, L. D.; Zawadsky, C.; Binnerup, S. J.; Øregaard, G.; Sørensen, S. J.; Kroer, N.

2008-01-01

Mercury-resistant bacteria may be important players in mercury biogeochemistry. To assess the potential for mercury reduction by two subsurface microbial communities, resistant subpopulations and their merA genes were characterized by a combined molecular and cultivation-dependent approach. The cultivation method simulated natural conditions by using polycarbonate membranes as a growth support and a nonsterile soil slurry as a culture medium. Resistant bacteria were pregrown to microcolony-forming units (mCFU) before being plated on standard medium. Compared to direct plating, culturability was increased up to 2,800 times and numbers of mCFU were similar to the total number of mercury-resistant bacteria in the soils. Denaturing gradient gel electrophoresis analysis of DNA extracted from membranes suggested stimulation of growth of hard-to-culture bacteria during the preincubation. A total of 25 different 16S rRNA gene sequences were observed, including Alpha-, Beta-, and Gammaproteobacteria; Actinobacteria; Firmicutes; and Bacteroidetes. The diversity of isolates obtained by direct plating included eight different 16S rRNA gene sequences (Alpha- and Betaproteobacteria and Actinobacteria). Partial sequencing of merA of selected isolates led to the discovery of new merA sequences. With phylum-specific merA primers, PCR products were obtained for Alpha- and Betaproteobacteria and Actinobacteria but not for Bacteroidetes and Firmicutes. The similarity to known sequences ranged between 89 and 95%. One of the sequences did not result in a match in the BLAST search. The results illustrate the power of integrating advanced cultivation methodology with molecular techniques for the characterization of the diversity of mercury-resistant populations and assessing the potential for mercury reduction in contaminated environments. PMID:18441111

Unique hyper-thermal composting process in Kagoshima City forms distinct bacterial community structures.

PubMed

Tashiro, Yukihiro; Tabata, Hanae; Itahara, Asuka; Shimizu, Natsuki; Tashiro, Kosuke; Sakai, Kenji

2016-11-01

A unique compost, Satsuma soil, is produced from three types of wastewater sludge using hyper-thermal processes at temperatures much higher than that of general thermophilic processes in Kagoshima City, Japan. We analyzed the bacterial community structures of this hyper-thermal compost sample and other sludges and composts by a high-throughput barcoded pyrosequencing method targeting the 16S rRNA gene. In total, 621,076 reads were derived from 17 samples and filtered. Artificial sequences were deleted and the reads were clustered based on the operational taxonomic units (OTUs) at 97% similarity. Phylum-level analysis of the hyper-thermal compost revealed drastic changes of the sludge structures (each relative abundance) from Firmicutes (average 47.8%), Proteobacteria (average 22.3%), and Bacteroidetes (average 10.1%) to two main phyla including Firmicutes (73.6%) and Actinobacteria (25.0%) with less Proteobacteria (∼0.3%) and Bacteroidetes (∼0.1%). Furthermore, we determined the predominant species (each relative abundance) of the hyper-thermal compost including Firmicutes related to Staphylococcus cohnii (13.8%), Jeotgalicoccus coquinae (8.01%), and Staphylococcus lentus (5.96%), and Actinobacteria related to Corynebacterium stationis (6.41%), and found that these species were not predominant in wastewater sludge. In contrast, we did not observe any common structures among eight other composts produced, using the hyper-thermal composts as the inoculums, under thermophilic conditions from different materials. Principle coordinate analysis of the hyper-thermal compost indicated a large difference in bacterial community structures from material sludge and other composts. These results suggested that a distinct bacterial community structure was formed by hyper-thermal composting. Copyright © 2016 The Society for Biotechnology, Japan. Published by Elsevier B.V. All rights reserved.

Cdc48-like protein of actinobacteria (Cpa) is a novel proteasome interactor in mycobacteria and related organisms.

PubMed

Ziemski, Michal; Jomaa, Ahmad; Mayer, Daniel; Rutz, Sonja; Giese, Christoph; Veprintsev, Dmitry; Weber-Ban, Eilika

2018-05-29

Cdc48 is a AAA+ ATPase that plays an essential role for many cellular processes in eukaryotic cells. An archaeal homologue of this highly conserved enzyme was shown to directly interact with the 20S proteasome. Here, we analyze the occurrence and phylogeny of a Cdc48 homologue in Actinobacteria and assess its cellular function and possible interaction with the bacterial proteasome. Our data demonstrate that Cdc48-like protein of actinobacteria (Cpa) forms hexameric rings and that the oligomeric state correlates directly with the ATPase activity. Furthermore, we show that the assembled Cpa rings can physically interact with the 20S core particle. Comparison of the Mycobacterium smegmatis wild-type with a cpa knockout strain under carbon starvation uncovers significant changes in the levels of around 500 proteins. Pathway mapping of the observed pattern of changes identifies ribosomal proteins as a particular hotspot, pointing amongst others toward a role of Cpa in ribosome adaptation during starvation. © 2018, Ziemski et al.

Genomics of Probiotic Bacteria

NASA Astrophysics Data System (ADS)

O'Flaherty, Sarah; Goh, Yong Jun; Klaenhammer, Todd R.

Probiotic bacteria from the Lactobacillus and Bifidobacterium species belong to the Firmicutes and the Actinobacteria phylum, respectively. Lactobacilli are members of the lactic acid bacteria (LAB) group, a broadly defined family of microorganisms that ferment various hexoses into primarily lactic acid. Lactobacilli are typically low G + C gram-positive species which are phylogenetically diverse, with over 100 species documented to date. Bifidobacteria are heterofermentative, high G + C content bacteria with about 30 species of bifidobacteria described to date.

4-alkyl-L-(Dehydro)proline biosynthesis in actinobacteria involves N-terminal nucleophile-hydrolase activity of γ-glutamyltranspeptidase homolog for C-C bond cleavage

NASA Astrophysics Data System (ADS)

Zhong, Guannan; Zhao, Qunfei; Zhang, Qinglin; Liu, Wen

2017-07-01

γ-Glutamyltranspeptidases (γ-GTs), ubiquitous in glutathione metabolism for γ-glutamyl transfer/hydrolysis, are N-terminal nucleophile (Ntn)-hydrolase fold proteins that share an autoproteolytic process for self-activation. γ-GT homologues are widely present in Gram-positive actinobacteria where their Ntn-hydrolase activities, however, are not involved in glutathione metabolism. Herein, we demonstrate that the formation of 4-Alkyl-L-(dehydro)proline (ALDP) residues, the non-proteinogenic α-amino acids that serve as vital components of many bioactive metabolites found in actinobacteria, involves unprecedented Ntn-hydrolase activity of γ-GT homologue for C-C bond cleavage. The related enzymes share a key Thr residue, which acts as an internal nucleophile for protein hydrolysis and then as a newly released N-terminal nucleophile for carboxylate side-chain processing likely through the generation of an oxalyl-Thr enzyme intermediate. These findings provide mechanistic insights into the biosynthesis of various ALDP residues/associated natural products, highlight the versatile functions of Ntn-hydrolase fold proteins, and particularly generate interest in thus far less-appreciated γ-GT homologues in actinobacteria.

Isolation, Characterization, and Antibacterial Activity of Hard-to-Culture Actinobacteria from Cave Moonmilk Deposits.

PubMed

Adam, Delphine; Maciejewska, Marta; Naômé, Aymeric; Martinet, Loïc; Coppieters, Wouter; Karim, Latifa; Baurain, Denis; Rigali, Sébastien

2018-03-22

Cave moonmilk deposits host an abundant and diverse actinobacterial population that has a great potential for producing novel natural bioactive compounds. In our previous attempt to isolate culturable moonmilk-dwelling Actinobacteria, only Streptomyces species were recovered, whereas a metagenetic study of the same deposits revealed a complex actinobacterial community including 46 actinobacterial genera in addition to streptomycetes. In this work, we applied the rehydration-centrifugation method to lessen the occurrence of filamentous species and tested a series of strategies to achieve the isolation of hard-to-culture and rare Actinobacteria from the moonmilk deposits of the cave "Grotte des Collemboles". From the "tips and tricks" that were tested, separate autoclaving of the components of the International Streptomyces Project (ISP) medium number 5 (ISP5) medium, prolonged incubation time, and dilution of the moonmilk suspension were found to most effectively improve colony forming units. Taxonomic analyses of the 40 isolates revealed new representatives of the Agromyces , Amycolatopsis , Kocuria , Micrococcus , Micromonospora , Nocardia , and Rhodococcus species, as well as additional new streptomycetes. The applied methodologies allowed the isolation of strains associated with both the least and most abundant moonmilk-dwelling actinobacterial operational taxonomic units. Finally, bioactivity screenings revealed that some isolates displayed high antibacterial activities, and genome mining uncovered a strong potential for the production of natural compounds.

Complete genome sequence of Terriglobus saanensis type strain SP1PR4T, an Acidobacteria from tundra soil

DOE Office of Scientific and Technical Information (OSTI.GOV)

Rawat, Suman R.; Mannisto, Minna; Starovoytov, Valentin

2012-01-01

Terriglobus saanensis SP1PR4T is a novel species of the genus Terriglobus. T. saanensis is of ecological interest because it is a representative of the phylum Acidobacteria, which are dominant members of bacterial soil microbiota in Arctic ecosystems. T. saanensis is a cold-adapted acidophile and a versatile heterotroph utilizing a suite of simple sugars and complex polysaccharides. The genome contained an abundance of genes assigned to metabolism and transport of carbohydrates including gene modules encoding for carbohydrate-active enzyme (CAZyme) family involved in breakdown, utilization and biosynthesis of diverse structural and storage polysaccharides. T. saanensis SP1PR4T represents the first member of genusmore » Terriglobus with a completed genome sequence, consisting of a single replicon of 5,095,226 base pairs (bp), 54 RNA genes and 4,279 protein-coding genes. We infer that the physiology and metabolic potential of T. saanensis is adapted to allow for resilience to the nutrient-deficient conditions and fluctuating temperatures of Arctic tundra soils.« less

Detection and molecular characterization of filamentous actinobacteria and thermoactinomycetes present in water-damaged building materials.

PubMed

Suihko, M-L; Priha, O; Alakomi, H-L; Thompson, P; Mälarstig, B; Stott, R; Richardson, M

2009-06-01

In this study the dominant filamentous actinobacteria occurring in water-damaged building materials were detected by culture and characterized by automated ribotyping and 16S rRNA gene sequencing. Fifty-two samples were taken from 20 water-damaged houses in four different countries. A total of 122 bacterial isolates were analyzed. Actinobacteria or thermoactinomycetes were present in 48% of the samples. The dominant genus was Streptomyces (58% of isolates), followed by Thermoactinomyces (23%), Laceyella (14%), Nocardiopsis (3%), Pseudonocardia (1%) and Saccharomonospora (1%). The most frequently detected species was the thermophilic Thermoactinomyces vulgaris (14 samples/4 countries). The most common streptomycetes were closely related to the heterogeneous species Streptomyces microflavus (7/2) or Streptomyces griseus (6/2). Automated ribotyping was a rapid tool for reliable characterization of these isolates. The spores of thermoactinomycetes and toxic substances of Nocardiopsis species and S. griseus may constitute a risk for human health. Harmful microbes in indoor environments are a cause of public concern. To develop rapid and simple-to-use molecular biological methods to detect the presence of harmful actinobacterial species in water-damaged buildings more information about their occurrence in those materials is needed, which this study provides.

A Combination of Extreme Environmental Conditions Favor the Prevalence of Endospore-Forming Firmicutes.

PubMed

Filippidou, Sevasti; Wunderlin, Tina; Junier, Thomas; Jeanneret, Nicole; Dorador, Cristina; Molina, Veronica; Johnson, David R; Junier, Pilar

2016-01-01

Environmental conditions unsuitable for microbial growth are the rule rather than the exception in most habitats. In response to this, microorganisms have developed various strategies to withstand environmental conditions that limit active growth. Endospore-forming Firmicutes (EFF) deploy a myriad of survival strategies in order to resist adverse conditions. Like many bacterial groups, they can form biofilms and detect nutrient scarcity through chemotaxis. Moreover, within this paraphyletic group of Firmicutes, ecophysiological optima are diverse. Nonetheless, a response to adversity that delimits this group is the formation of wet-heat resistant spores. These strategies are energetically demanding and therefore might affect the biological success of EFF. Therefore, we hypothesize that abundance and diversity of EFF should be maximized in those environments in which the benefits of these survival strategies offsets the energetic cost. In order to address this hypothesis, geothermal and mineral springs and drillings were selected because in these environments of steep physicochemical gradients, diversified survival strategies may become a successful strategy.We collected 71 samples from geothermal and mineral environments characterized by none (null), single or multiple limiting environmental factors (temperature, pH, UV radiation, and specific mineral composition). To measure success, we quantified EFF gene copy numbers (GCN; spo0A gene) in relation to total bacterial GCN (16S rRNA gene), as well as the contribution of EFF to community composition. The quantification showed that relative GCN for EFF reached up to 20% at sites characterized by multiple limiting environmental factors, whereas it corresponded to less than 1% at sites with one or no limiting environmental factor. Pyrosequencing of the 16S rRNA gene supports a higher contribution of EFF at sites with multiple limiting factors. Community composition suggested a combination of phylotypes for which active

A Combination of Extreme Environmental Conditions Favor the Prevalence of Endospore-Forming Firmicutes

PubMed Central

Filippidou, Sevasti; Wunderlin, Tina; Junier, Thomas; Jeanneret, Nicole; Dorador, Cristina; Molina, Veronica; Johnson, David R.; Junier, Pilar

2016-01-01

Environmental conditions unsuitable for microbial growth are the rule rather than the exception in most habitats. In response to this, microorganisms have developed various strategies to withstand environmental conditions that limit active growth. Endospore-forming Firmicutes (EFF) deploy a myriad of survival strategies in order to resist adverse conditions. Like many bacterial groups, they can form biofilms and detect nutrient scarcity through chemotaxis. Moreover, within this paraphyletic group of Firmicutes, ecophysiological optima are diverse. Nonetheless, a response to adversity that delimits this group is the formation of wet-heat resistant spores. These strategies are energetically demanding and therefore might affect the biological success of EFF. Therefore, we hypothesize that abundance and diversity of EFF should be maximized in those environments in which the benefits of these survival strategies offsets the energetic cost. In order to address this hypothesis, geothermal and mineral springs and drillings were selected because in these environments of steep physicochemical gradients, diversified survival strategies may become a successful strategy.We collected 71 samples from geothermal and mineral environments characterized by none (null), single or multiple limiting environmental factors (temperature, pH, UV radiation, and specific mineral composition). To measure success, we quantified EFF gene copy numbers (GCN; spo0A gene) in relation to total bacterial GCN (16S rRNA gene), as well as the contribution of EFF to community composition. The quantification showed that relative GCN for EFF reached up to 20% at sites characterized by multiple limiting environmental factors, whereas it corresponded to less than 1% at sites with one or no limiting environmental factor. Pyrosequencing of the 16S rRNA gene supports a higher contribution of EFF at sites with multiple limiting factors. Community composition suggested a combination of phylotypes for which active

Diversity of Culturable Thermophilic Actinobacteria in Hot Springs in Tengchong, China and Studies of their Biosynthetic Gene Profiles.

PubMed

Liu, Lan; Salam, Nimaichand; Jiao, Jian-Yu; Jiang, Hong-Chen; Zhou, En-Min; Yin, Yi-Rui; Ming, Hong; Li, Wen-Jun

2016-07-01

The class Actinobacteria has been a goldmine for the discovery of antibiotics and has attracted interest from both academics and industries. However, an absence of novel approaches during the last few decades has limited the discovery of new microbial natural products useful for industries. Scientists are now focusing on the ecological aspects of diverse environments including unexplored or underexplored habitats and extreme environments in the search for new metabolites. This paper reports on the diversity of culturable actinobacteria associated with hot springs located in Tengchong County, Yunnan Province, southwestern China. A total of 58 thermophilic actinobacterial strains were isolated from the samples collected from ten hot springs distributed over three geothermal fields (e.g., Hehua, Rehai, and Ruidian). Phylogenetic positions and their biosynthetic profiles were analyzed by sequencing 16S rRNA gene and three biosynthetic gene clusters (KS domain of PKS-I, KSα domain of PKS-II and A domain of NRPS). On the basis of 16S rRNA gene phylogenetic analysis, the 58 strains were affiliated with 12 actinobacterial genera: Actinomadura Micromonospora, Microbispora, Micrococcus, Nocardiopsis, Nonomuraea, Promicromonospora, Pseudonocardia, Streptomyces, Thermoactinospora, Thermocatellispora, and Verrucosispora, of which the two novel genera Thermoactinospora and Thermocatellisopora were recently described from among these strains. Considering the biosynthetic potential of these actinobacterial strains, 22 were positive for PCR amplification of at least one of the three biosynthetic gene clusters (PKS-I, PKS-II, and NRPS). These actinobacteria were further subjected to antimicrobial assay against five opportunistic human pathogens (Acinetobacter baumannii, Escherichia coli, Micrococcus luteus, Staphylococcus aureus and Streptococcus faecalis). All of the 22 strains that were positive for PCR amplification of at least one of the biosynthetic gene domains exhibited

Coastal bacterioplankton community diversity along a latitudinal gradient in Latin America by means of V6 tag pyrosequencing.

PubMed

Thompson, Fabiano L; Bruce, Thiago; Gonzalez, Alessandra; Cardoso, Alexander; Clementino, Maysa; Costagliola, Marcela; Hozbor, Constanza; Otero, Ernesto; Piccini, Claudia; Peressutti, Silvia; Schmieder, Robert; Edwards, Robert; Smith, Mathew; Takiyama, Luis Roberto; Vieira, Ricardo; Paranhos, Rodolfo; Artigas, Luis Felipe

2011-02-01

The bacterioplankton diversity of coastal waters along a latitudinal gradient between Puerto Rico and Argentina was analyzed using a total of 134,197 high-quality sequences from the V6 hypervariable region of the small-subunit ribosomal RNA gene (16S rRNA) (mean length of 60 nt). Most of the OTUs were identified into Proteobacteria, Bacteriodetes, Cyanobacteria, and Actinobacteria, corresponding to approx. 80% of the total number of sequences. The number of OTUs corresponding to species varied between 937 and 1946 in the seven locations. Proteobacteria appeared at high frequency in the seven locations. An enrichment of Cyanobacteria was observed in Puerto Rico, whereas an enrichment of Bacteroidetes was detected in the Argentinian shelf and Uruguayan coastal lagoons. The highest number of sequences of Actinobacteria and Acidobacteria were obtained in the Amazon estuary mouth. The rarefaction curves and Good coverage estimator for species diversity suggested a significant coverage, with values ranging between 92 and 97% for Good coverage. Conserved taxa corresponded to aprox. 52% of all sequences. This study suggests that human-contaminated environments may influence bacterioplankton diversity.

High‑throughput sequencing analyses of oral microbial diversity in healthy people and patients with dental caries and periodontal disease.

PubMed

Chen, Tingtao; Shi, Yan; Wang, Xiaolei; Wang, Xin; Meng, Fanjing; Yang, Shaoguo; Yang, Jian; Xin, Hongbo

2017-07-01

Recurrence of oral diseases caused by antibiotics has brought about an urgent requirement to explore the oral microbial diversity in the human oral cavity. In the present study, the high‑throughput sequencing method was adopted to compare the microbial diversity of healthy people and oral patients and sequence analysis was performed by UPARSE software package. The Venn results indicated that a mean of 315 operational taxonomic units (OTUs) was obtained, and 73, 64, 53, 19 and 18 common OTUs belonging to Firmicutes, Bacteroidetes, Proteobacteria, Actinobacteria and Fusobacteria, respectively, were identified in healthy people. Moreover, the reduction of Firmicutes and the increase of Proteobacteria in the children group, and the increase of Firmicutes and the reduction of Proteobacteria in the youth and adult groups, indicated that the age bracket and oral disease had largely influenced the tooth development and microbial development in the oral cavity. In addition, the traditional 'pathogenic bacteria' of Firmicutes, Proteobacteria and Bacteroidetes (accounted for >95% of the total sequencing number in each group) indicated that the 'harmful' bacteria may exert beneficial effects on oral health. Therefore, the data will provide certain clues for curing some oral diseases by the strategy of adjusting the disturbed microbial compositions in oral disease to healthy level.

Characterization of atmospheric bioaerosols along the transport pathway of Asian dust during the Dust-Bioaerosol 2016 Campaign

NASA Astrophysics Data System (ADS)

Tang, Kai; Huang, Zhongwei; Huang, Jianping; Maki, Teruya; Zhang, Shuang; Shimizu, Atsushi; Ma, Xiaojun; Shi, Jinsen; Bi, Jianrong; Zhou, Tian; Wang, Guoyin; Zhang, Lei

2018-05-01

Previous studies have shown that bioaerosols are injected into the atmosphere during dust events. These bioaerosols may affect leeward ecosystems, human health, and agricultural productivity and may even induce climate change. However, bioaerosol dynamics have rarely been investigated along the transport pathway of Asian dust, especially in China where dust events affect huge areas and massive numbers of people. Given this situation, the Dust-Bioaerosol (DuBi) Campaign was carried out over northern China, and the effects of dust events on the amount and diversity of bioaerosols were investigated. The results indicate that the number of bacteria showed remarkable increases during the dust events, and the diversity of the bacterial communities also increased significantly, as determined by means of microscopic observations with 4,6-diamidino-2-phenylindole (DAPI) staining and MiSeq sequencing analysis. These results indicate that dust clouds can carry many bacteria of various types into downwind regions and may have potentially important impacts on ecological environments and climate change. The abundances of DAPI-stained bacteria in the dust samples were 1 to 2 orders of magnitude greater than those in the non-dust samples and reached 105-106 particles m-3. Moreover, the concentration ratios of DAPI-stained bacteria to yellow fluorescent particles increased from 5.1 % ± 6.3 % (non-dust samples) to 9.8 % ± 6.3 % (dust samples). A beta diversity analysis of the bacterial communities demonstrated the distinct clustering of separate prokaryotic communities in the dust and non-dust samples. Actinobacteria, Bacteroidetes, and Proteobacteria remained the dominant phyla in all samples. As for Erenhot, the relative abundances of Acidobacteria and Chloroflexi had a remarkable rise in dust events. In contrast, the relative abundances of Acidobacteria and Chloroflexi in non-dust samples of R-DzToUb were greater than those in dust samples. Alphaproteobacteria made the major

The Role of Bacillithiol in Gram-Positive Firmicutes

PubMed Central

Chandrangsu, Pete; Loi, Vu Van

2018-01-01

Abstract Significance: Since the discovery and structural characterization of bacillithiol (BSH), the biochemical functions of BSH-biosynthesis enzymes (BshA/B/C) and BSH-dependent detoxification enzymes (FosB, Bst, GlxA/B) have been explored in Bacillus and Staphylococcus species. It was shown that BSH plays an important role in detoxification of reactive oxygen and electrophilic species, alkylating agents, toxins, and antibiotics. Recent Advances: More recently, new functions of BSH were discovered in metal homeostasis (Zn buffering, Fe-sulfur cluster, and copper homeostasis) and virulence control in Staphylococcus aureus. Unexpectedly, strains of the S. aureus NCTC8325 lineage were identified as natural BSH-deficient mutants. Modern mass spectrometry-based approaches have revealed the global reach of protein S-bacillithiolation in Firmicutes as an important regulatory redox modification under hypochlorite stress. S-bacillithiolation of OhrR, MetE, and glyceraldehyde-3-phosphate dehydrogenase (Gap) functions, analogous to S-glutathionylation, as both a redox-regulatory device and in thiol protection under oxidative stress. Critical Issues: Although the functions of the bacilliredoxin (Brx) pathways in the reversal of S-bacillithiolations have been recently addressed, significantly more work is needed to establish the complete Brx reduction pathway, including the major enzyme(s), for reduction of oxidized BSH (BSSB) and the targets of Brx action in vivo. Future Directions: Despite the large number of identified S-bacillithiolated proteins, the physiological relevance of this redox modification was shown for only selected targets and should be a subject of future studies. In addition, many more BSH-dependent detoxification enzymes are evident from previous studies, although their roles and biochemical mechanisms require further study. This review of BSH research also pin-points these missing gaps for future research. Antioxid. Redox Signal. 28, 445–462. PMID

Survival of introduced phosphate-solubilizing bacteria (PSB) and their impact on microbial community structure during the phytoextraction of Cd-contaminated soil.

PubMed

Jeong, Seulki; Moon, Hee Sun; Shin, Doyun; Nam, Kyoungphile

2013-12-15

This study was conducted to investigate whether or not phosphate-solubilizing bacteria (PSB) as a kind of plant growth promoting rhizobacteria enhance the uptake of Cd by plants. In addition, the effect of PSB augmentation during phytoextraction on the microbial community of indigenous soil bacteria was also studied. In the initial Cd-contaminated soil, the major phyla were Proteobacteria (35%), Actinobacteria (38%) and Firmicutes (8%). While Proteobacteria were dominant at the second and sixth week (41 and 54%, respectively) in inoculated soil, Firmicutes (mainly belonging to the Bacilli class-61%), dramatically increased in the eight-week soil. For the uninoculated soil, the proportion of α-Proteobacteria increased after eight weeks (32%). Interestingly, Actinobacteria class, which was originally present in the soil (37%), seemed to disappear during phytoremediation, irrespective of whether PSB was inoculated or not. Cluster analysis and Principal Component Analysis revealed that the microbial community of eight-week inoculated soil was completely separated from the other soil samples, due to the dramatic increase of Bacillus aryabhattai. These findings revealed that it took at least eight weeks for the inoculated Bacillus sp. to functionally adapt to the introduced soil, against competition with indigenous microorganisms in soil. An ecological understanding of interaction among augmented bacteria, plant and indigenous soil bacteria is needed, for proper management of phytoextraction. Copyright © 2013 Elsevier B.V. All rights reserved.

Ambient Ultrafine Particle Ingestion Alters Gut Microbiota in Association with Increased Atherogenic Lipid Metabolites

PubMed Central

Li, Rongsong; Yang, Jieping; Saffari, Arian; Jacobs, Jonathan; Baek, Kyung In; Hough, Greg; Larauche, Muriel H.; Ma, Jianguo; Jen, Nelson; Moussaoui, Nabila; Zhou, Bill; Kang, Hanul; Reddy, Srinivasa; Henning, Susanne M.; Campen, Matthew J.; Pisegna, Joseph; Li, Zhaoping; Fogelman, Alan M.; Sioutas, Constantinos; Navab, Mohamad; Hsiai, Tzung K.

2017-01-01

Ambient particulate matter (PM) exposure is associated with atherosclerosis and inflammatory bowel disease. Ultrafine particles (UFP, dp < 0.1–0.2 μm) are redox active components of PM. We hypothesized that orally ingested UFP promoted atherogenic lipid metabolites in both the intestine and plasma via altered gut microbiota composition. Low density lipoprotein receptor-null (Ldlr−/−) mice on a high-fat diet were orally administered with vehicle control or UFP (40 μg/mouse/day) for 3 days a week. After 10 weeks, UFP ingested mice developed macrophage and neutrophil infiltration in the intestinal villi, accompanied by elevated cholesterol but reduced coprostanol levels in the cecum, as well as elevated atherogenic lysophosphatidylcholine (LPC 18:1) and lysophosphatidic acids (LPAs) in the intestine and plasma. At the phylum level, Principle Component Analysis revealed significant segregation of microbiota compositions which was validated by Beta diversity analysis. UFP-exposed mice developed increased abundance in Verrocomicrobia but decreased Actinobacteria, Cyanobacteria, and Firmicutes as well as a reduced diversity in microbiome. Spearman’s analysis negatively correlated Actinobacteria with cecal cholesterol, intestinal and plasma LPC18:1, and Firmicutes and Cyanobacteria with plasma LPC 18:1. Thus, ultrafine particles ingestion alters gut microbiota composition, accompanied by increased atherogenic lipid metabolites. These findings implicate the gut-vascular axis in a atherosclerosis model. PMID:28211537

Different continuous cropping spans significantly affect microbial community membership and structure in a vanilla-grown soil as revealed by deep pyrosequencing.

PubMed

Xiong, Wu; Zhao, Qingyun; Zhao, Jun; Xun, Weibing; Li, Rong; Zhang, Ruifu; Wu, Huasong; Shen, Qirong

2015-07-01

In the present study, soil bacterial and fungal communities across vanilla continuous cropping time-series fields were assessed through deep pyrosequencing of 16S ribosomal RNA (rRNA) genes and internal transcribed spacer (ITS) regions. The results demonstrated that the long-term monoculture of vanilla significantly altered soil microbial communities. Soil fungal diversity index increased with consecutive cropping years, whereas soil bacterial diversity was relatively stable. Bray-Curtis dissimilarity cluster and UniFrac-weighted principal coordinate analysis (PCoA) revealed that monoculture time was the major determinant for fungal community structure, but not for bacterial community structure. The relative abundances (RAs) of the Firmicutes, Actinobacteria, Bacteroidetes, and Basidiomycota phyla were depleted along the years of vanilla monoculture. Pearson correlations at the phyla level demonstrated that Actinobacteria, Armatimonadetes, Bacteroidetes, Verrucomicrobia, and Firmicutes had significant negative correlations with vanilla disease index (DI), while no significant correlation for fungal phyla was observed. In addition, the amount of the pathogen Fusarium oxysporum accumulated with increasing years and was significantly positively correlated with vanilla DI. By contrast, the abundance of beneficial bacteria, including Bradyrhizobium and Bacillus, significantly decreased over time. In sum, soil weakness and vanilla stem wilt disease after long-term continuous cropping can be attributed to the alteration of the soil microbial community membership and structure, i.e., the reduction of the beneficial microbes and the accumulation of the fungal pathogen.

Diversity, Novelty, and Antimicrobial Activity of Endophytic Actinobacteria From Mangrove Plants in Beilun Estuary National Nature Reserve of Guangxi, China.

PubMed

Jiang, Zhong-Ke; Tuo, Li; Huang, Da-Lin; Osterman, Ilya A; Tyurin, Anton P; Liu, Shao-Wei; Lukyanov, Dmitry A; Sergiev, Petr V; Dontsova, Olga A; Korshun, Vladimir A; Li, Fei-Na; Sun, Cheng-Hang

2018-01-01

Endophytic actinobacteria are one of the important pharmaceutical resources and well known for producing different types of bioactive substances. Nevertheless, detection of the novelty, diversity, and bioactivity on endophytic actinobacteria isolated from mangrove plants are scarce. In this study, five different mangrove plants, Avicennia marina, Aegiceras corniculatum, Kandelia obovota, Bruguiera gymnorrhiza , and Thespesia populnea , were collected from Beilun Estuary National Nature Reserve in Guangxi Zhuang Autonomous Region, China. A total of 101 endophytic actinobacteria strains were recovered by culture-based approaches. They distributed in 7 orders, 15 families, and 28 genera including Streptomyces, Curtobacterium, Mycobacterium, Micrococcus, Brevibacterium, Kocuria, Nocardioides, Kineococcus, Kytococcus, Marmoricola, Microbacterium, Micromonospora, Actinoplanes, Agrococcus, Amnibacterium, Brachybacterium, Citricoccus, Dermacoccus, Glutamicibacter, Gordonia, Isoptericola, Janibacter, Leucobacter, Nocardia, Nocardiopsis, Pseudokineococcus, Sanguibacter , and Verrucosispora . Among them, seven strains were potentially new species of genera Nocardioides, Streptomyces, Amnibacterium, Marmoricola , and Mycobacterium . Above all, strain 8BXZ-J1 has already been characterized as a new species of the genus Marmoricola . A total of 63 out of 101 strains were chosen to screen antibacterial activities by paper-disk diffusion method and inhibitors of ribosome and DNA biosynthesis by means of a double fluorescent protein reporter. A total of 31 strains exhibited positive results in at least one antibacterial assay. Notably, strain 8BXZ-J1 and three other potential novel species, 7BMP-1, 5BQP-J3, and 1BXZ-J1, all showed antibacterial bioactivity. In addition, 21 strains showed inhibitory activities against at least one "ESKAPE" resistant pathogens. We also found that Streptomyces strains 2BBP-J2 and 1BBP-1 produce bioactive compound with inhibitory activity on protein

Diversity, Novelty, and Antimicrobial Activity of Endophytic Actinobacteria From Mangrove Plants in Beilun Estuary National Nature Reserve of Guangxi, China

PubMed Central

Jiang, Zhong-ke; Tuo, Li; Huang, Da-lin; Osterman, Ilya A.; Tyurin, Anton P.; Liu, Shao-wei; Lukyanov, Dmitry A.; Sergiev, Petr V.; Dontsova, Olga A.; Korshun, Vladimir A.; Li, Fei-na; Sun, Cheng-hang

2018-01-01

Endophytic actinobacteria are one of the important pharmaceutical resources and well known for producing different types of bioactive substances. Nevertheless, detection of the novelty, diversity, and bioactivity on endophytic actinobacteria isolated from mangrove plants are scarce. In this study, five different mangrove plants, Avicennia marina, Aegiceras corniculatum, Kandelia obovota, Bruguiera gymnorrhiza, and Thespesia populnea, were collected from Beilun Estuary National Nature Reserve in Guangxi Zhuang Autonomous Region, China. A total of 101 endophytic actinobacteria strains were recovered by culture-based approaches. They distributed in 7 orders, 15 families, and 28 genera including Streptomyces, Curtobacterium, Mycobacterium, Micrococcus, Brevibacterium, Kocuria, Nocardioides, Kineococcus, Kytococcus, Marmoricola, Microbacterium, Micromonospora, Actinoplanes, Agrococcus, Amnibacterium, Brachybacterium, Citricoccus, Dermacoccus, Glutamicibacter, Gordonia, Isoptericola, Janibacter, Leucobacter, Nocardia, Nocardiopsis, Pseudokineococcus, Sanguibacter, and Verrucosispora. Among them, seven strains were potentially new species of genera Nocardioides, Streptomyces, Amnibacterium, Marmoricola, and Mycobacterium. Above all, strain 8BXZ-J1 has already been characterized as a new species of the genus Marmoricola. A total of 63 out of 101 strains were chosen to screen antibacterial activities by paper-disk diffusion method and inhibitors of ribosome and DNA biosynthesis by means of a double fluorescent protein reporter. A total of 31 strains exhibited positive results in at least one antibacterial assay. Notably, strain 8BXZ-J1 and three other potential novel species, 7BMP-1, 5BQP-J3, and 1BXZ-J1, all showed antibacterial bioactivity. In addition, 21 strains showed inhibitory activities against at least one “ESKAPE” resistant pathogens. We also found that Streptomyces strains 2BBP-J2 and 1BBP-1 produce bioactive compound with inhibitory activity on protein

Dysbiosis of the Fecal Microbiota in Cattle Infected with Mycobacterium avium subsp. paratuberculosis

PubMed Central

Vecchiarelli, Bonnie; Indugu, Nagaraju; Kumar, Sanjay; Gallagher, Susan C.; Fyock, Terry L.; Sweeney, Raymond W.

2016-01-01

Johne's disease (JD) is a chronic, intestinal infection of cattle, caused by Mycobacterium avium subsp. paratuberculosis (MAP). It results in granulomatous inflammation of the intestinal lining, leading to malabsorption, diarrhea, and weight loss. Crohn’s disease (CD), a chronic, inflammatory gastrointestinal disease of humans, has many clinical and pathologic similarities to JD. Dysbiosis of the enteric microbiota has been demonstrated in CD patients. It is speculated that this dysbiosis may contribute to the intestinal inflammation observed in those patients. The purpose of this study was to investigate the diversity patterns of fecal bacterial populations in cattle infected with MAP, compared to those of uninfected control cattle, using phylogenomic analysis. Fecal samples were selected to include samples from 20 MAP-positive cows; 25 MAP-negative herdmates; and 25 MAP-negative cows from a MAP-free herd. The genomic DNA was extracted; PCR amplified sequenced on a 454 Roche platform, and analyzed using QIIME. Approximately 199,077 reads were analyzed from 70 bacterial communities (average of 2,843 reads/sample). The composition of bacterial communities differed between the 3 treatment groups (P < 0.001; Permanova test). Taxonomic assignment of the operational taxonomic units (OTUs) identified 17 bacterial phyla across all samples. Bacteroidetes and Firmicutes constituted more than 95% of the bacterial population in the negative and exposed groups. In the positive group, lineages of Actinobacteria and Proteobacteria increased and those of Bacteroidetes and Firmicutes decreased (P < 0.001). Actinobacteria was highly abundant (30% of the total bacteria) in the positive group compared to exposed and negative groups (0.1–0.2%). Notably, the genus Arthrobacter was found to predominate Actinobacteria in the positive group. This study indicates that MAP-infected cattle have a different composition of their fecal microbiota than MAP-negative cattle. PMID:27494144

Dysbiosis of the Fecal Microbiota in Cattle Infected with Mycobacterium avium subsp. paratuberculosis.

PubMed

Fecteau, Marie-Eve; Pitta, Dipti W; Vecchiarelli, Bonnie; Indugu, Nagaraju; Kumar, Sanjay; Gallagher, Susan C; Fyock, Terry L; Sweeney, Raymond W

2016-01-01

Johne's disease (JD) is a chronic, intestinal infection of cattle, caused by Mycobacterium avium subsp. paratuberculosis (MAP). It results in granulomatous inflammation of the intestinal lining, leading to malabsorption, diarrhea, and weight loss. Crohn's disease (CD), a chronic, inflammatory gastrointestinal disease of humans, has many clinical and pathologic similarities to JD. Dysbiosis of the enteric microbiota has been demonstrated in CD patients. It is speculated that this dysbiosis may contribute to the intestinal inflammation observed in those patients. The purpose of this study was to investigate the diversity patterns of fecal bacterial populations in cattle infected with MAP, compared to those of uninfected control cattle, using phylogenomic analysis. Fecal samples were selected to include samples from 20 MAP-positive cows; 25 MAP-negative herdmates; and 25 MAP-negative cows from a MAP-free herd. The genomic DNA was extracted; PCR amplified sequenced on a 454 Roche platform, and analyzed using QIIME. Approximately 199,077 reads were analyzed from 70 bacterial communities (average of 2,843 reads/sample). The composition of bacterial communities differed between the 3 treatment groups (P < 0.001; Permanova test). Taxonomic assignment of the operational taxonomic units (OTUs) identified 17 bacterial phyla across all samples. Bacteroidetes and Firmicutes constituted more than 95% of the bacterial population in the negative and exposed groups. In the positive group, lineages of Actinobacteria and Proteobacteria increased and those of Bacteroidetes and Firmicutes decreased (P < 0.001). Actinobacteria was highly abundant (30% of the total bacteria) in the positive group compared to exposed and negative groups (0.1-0.2%). Notably, the genus Arthrobacter was found to predominate Actinobacteria in the positive group. This study indicates that MAP-infected cattle have a different composition of their fecal microbiota than MAP-negative cattle.

De novo synthesis and functional analysis of the phosphatase-encoding gene acI-B of uncultured Actinobacteria from Lake Stechlin (NE Germany).

PubMed

Srivastava, Abhishek; McMahon, Katherine D; Stepanauskas, Ramunas; Grossart, Hans-Peter

2015-12-01

The National Center for Biotechnology Information [http://www.ncbi.nlm.nih.gov/guide/taxonomy/] database enlists more than 15,500 bacterial species. But this also includes a plethora of uncultured bacterial representations. Owing to their metabolism, they directly influence biogeochemical cycles, which underscores the the important status of bacteria on our planet. To study the function of a gene from an uncultured bacterium, we have undertaken a de novo gene synthesis approach. Actinobacteria of the acI-B subcluster are important but yet uncultured members of the bacterioplankton in temperate lakes of the northern hemisphere such as oligotrophic Lake Stechlin (NE Germany). This lake is relatively poor in phosphate (P) and harbors on average ~1.3 x 10 6 bacterial cells/ml, whereby Actinobacteria of the ac-I lineage can contribute to almost half of the entire bacterial community depending on seasonal variability. Single cell genome analysis of Actinobacterium SCGC AB141-P03, a member of the acI-B tribe in Lake Stechlin has revealed several phosphate-metabolizing genes. The genome of acI-B Actinobacteria indicates potential to degrade polyphosphate compound. To test for this genetic potential, we targeted the exoP-annotated gene potentially encoding polyphosphatase and synthesized it artificially to examine its biochemical role. Heterologous overexpression of the gene in Escherichia coli and protein purification revealed phosphatase activity. Comparative genome analysis suggested that homologs of this gene should be also present in other Actinobacteria of the acI lineages. This strategic retention of specialized genes in their genome provides a metabolic advantage over other members of the aquatic food web in a P-limited ecosystem. [Int Microbiol 2016; 19(1):39-47]. Copyright© by the Spanish Society for Microbiology and Institute for Catalan Studies.

Faecal microbiota of healthy adults in south India: Comparison of a tribal & a rural population.

PubMed

Ramadass, Balamurugan; Rani, B Sandya; Pugazhendhi, Srinivasan; John, K R; Ramakrishna, Balakrishnan S

2017-02-01

The relevance of the gut microbiota to human health is increasingly appreciated. The objective of this study was to compare the gut microbiota of a group of adult tribals with that of healthy adult villagers in Tamil Nadu, India. Faeces were collected from 10 healthy tribal adults (TAs) in the Jawadhi hills and from 10 healthy villagers [rural adults (RAs)] in Vellore district, Tamil Nadu. DNA was extracted, and 456 bp segments comprising hypervariable regions 3 and 4 of the 16S rRNA gene were amplified, barcoded and 454 sequenced. Totally 227,710 good-quality reads were analyzed. TAs consumed a millets-based diet, ate pork every day, and did not consume milk or milk products. RAs consumed a rice-based diet with meat intake once a week. In both groups, Firmicutes was the most abundant phylum, followed by Proteobacteria, Bacteroidetes and Actinobacteria. The median Firmicutes-to-Bacteroidetes ratio was 34.0 in TA and 92.9 in RA groups. Actinobacteria were significantly low in TA, possibly due to non-consumption of milk. Clostridium constituted the most abundant genus in both groups, but was significantly more abundant in TAs than RAs, while Streptococcus was significantly more abundant in RA (P<0.05). Analyses of genetic distance revealed that the microbiota were distinctly different between TA and RA, and principal component analysis using 550 distinct taxonomically identifiable sequences revealed a clear separation of microbiota composition in the two groups. Phylogenetic analysis of major microbiota indicated clustering of microbial groups at different major branch points for TAs and RAs. Phylum Firmicutes and genus Clostridium constituted the bulk of the faecal microbiota, while significant differences in composition between the groups were probably due to differences in diet and lifestyle.

Faecal microbiota of healthy adults in south India: Comparison of a tribal & a rural population

PubMed Central

Ramadass, Balamurugan; Rani, B. Sandya; Pugazhendhi, Srinivasan; John, K.R.; Ramakrishna, Balakrishnan S.

2017-01-01

Background & objectives: The relevance of the gut microbiota to human health is increasingly appreciated. The objective of this study was to compare the gut microbiota of a group of adult tribals with that of healthy adult villagers in Tamil Nadu, India. Methods: Faeces were collected from 10 healthy tribal adults (TAs) in the Jawadhi hills and from 10 healthy villagers [rural adults (RAs)] in Vellore district, Tamil Nadu. DNA was extracted, and 456 bp segments comprising hypervariable regions 3 and 4 of the 16S rRNA gene were amplified, barcoded and 454 sequenced. Results: Totally 227,710 good-quality reads were analyzed. TAs consumed a millets-based diet, ate pork every day, and did not consume milk or milk products. RAs consumed a rice-based diet with meat intake once a week. In both groups, Firmicutes was the most abundant phylum, followed by Proteobacteria, Bacteroidetes and Actinobacteria. The median Firmicutes-to-Bacteroidetes ratio was 34.0 in TA and 92.9 in RA groups. Actinobacteria were significantly low in TA, possibly due to non-consumption of milk. Clostridium constituted the most abundant genus in both groups, but was significantly more abundant in TAs than RAs, while Streptococcus was significantly more abundant in RA (P<0.05). Analyses of genetic distance revealed that the microbiota were distinctly different between TA and RA, and principal component analysis using 550 distinct taxonomically identifiable sequences revealed a clear separation of microbiota composition in the two groups. Phylogenetic analysis of major microbiota indicated clustering of microbial groups at different major branch points for TAs and RAs. Interpretation & conclusions: Phylum Firmicutes and genus Clostridium constituted the bulk of the faecal microbiota, while significant differences in composition between the groups were probably due to differences in diet and lifestyle. PMID:28639601

Resistance to and Accumulation of Heavy Metals by Actinobacteria Isolated from Abandoned Mining Areas

PubMed Central

El Baz, Soraia; Baz, Mohamed; El Gharmali, Abdelhay; Imziln, Boujamâa

2015-01-01

Accumulation of high concentrations of heavy metals in environments can cause many human health risks and serious ecological problems. Nowadays, bioremediation using microorganisms is receiving much attention due to their good performance. The aim of this work is to investigate heavy metals resistance and bioaccumulation potential of actinobacteria strains isolated from some abandoned mining areas. Analysis of mining residues revealed that high concentration of zinc “Zn” was recorded in Sidi Bouatman, Arbar, and Bir Nhass mining residues. The highest concentration of lead “Pb” was found in Sidi Bouatman. Copper “Cu,” cadmium “Cd,” and chromium “Cr” were found with moderate and low concentrations. The resistance of 59 isolated actinobacteria to the five heavy metals was also determined. Using molecular identification 16S rRNA, these 27 isolates were found to belong to Streptomyces and Amycolatopsis genera. The results showed different levels of heavy metal resistance; the minimum inhibitory concentration (MIC) recorded was 0.55 for Pb, 0.15 for Cr, and 0.10 mg·mL−1 for both Zn and Cu. Chemical precipitation assay of heavy metals using hydrogen sulfide technic (H2S) revealed that only 27 isolates have a strong ability to accumulate Pb (up to 600 mg of Pb per g of biomass for Streptomyces sp. BN3). PMID:25763383

Actinobacteria Isolated from an Underground Lake and Moonmilk Speleothem from the Biggest Conglomeratic Karstic Cave in Siberia as Sources of Novel Biologically Active Compounds

PubMed Central

Tokovenko, Bogdan T.; Protasov, Eugeniy S.; Gamaiunov, Stanislav V.; Rebets, Yuriy V.; Luzhetskyy, Andriy N.; Timofeyev, Maxim A.

2016-01-01

Actinobacteria isolated from unstudied ecosystems are one of the most interesting and promising sources of novel biologically active compounds. Cave ecosystems are unusual and rarely studied. Here, we report the isolation and characterization of ten new actinobacteria strains isolated from an ancient underground lake and moonmilk speleothem from the biggest conglomeratic karstic cave in Siberia with a focus on the biological activity of the obtained strains and the metabolite dereplication of one active strain. Streptomyces genera isolates from moonmilk speleothem demonstrated antibacterial and antifungal activities. Some of the strains were able to inhibit the growth of pathogenic Candida albicans. PMID:26901168

Effect of reclamation of abandoned salinized farmland on soil bacterial communities in arid northwest China.

PubMed

Cheng, Zhibo; Chen, Yun; Zhang, Fenghua

2018-07-15

Understanding the impact of reclamation of abandoned salinized farmland on soil bacterial community is of great importance for maintaining soil health and sustainability in arid regions. In this study, we used field sampling and 454 pyrosequencing methods to investigate the effects of 5-year reclamation treatments on soil properties, bacterial community composition and diversity. The four reclamation treatments are: abandoned salinized farmland (CK), cropland (CL), grassland (GL) and woodland (WL). We have found soil properties are significantly altered by abandoned salinized farmland reclamation. In particular, the lowest soil pH and electrical conductivity (EC) values are observed in CL (P<0.05). The dominant phyla are Firmicutes, Proteobacteria, Chloroflexi, Actinobacteria and Acidobacteria in all treatments. At the genus levels, the relative abundance of Bacillus, Lactococcus, Streptococcus and Enterococcus in CK, GL and WL is significantly higher than in CL. Bacterial diversity indices (i.e. ACE, Chao and Shannon) dramatically increase after the reclamation, with the highest in CL. Similar patterns of bacterial communities have been observed in CK, GL and WL soils, but significantly different from CL. Regression analyses indicate that the relative abundance of these phyla are significantly correlated with soil Fe, pH and EC. Results from non-metric multidimensional scaling (NMDS) and redundancy analysis (RDA) indicate that soil Fe content, EC and pH are the most important factors in shaping soil bacterial communities. Overall, results indicate that abandoned salinized farmland reclaimed for CL significantly decrease soil pH and EC, and increase soil bacterial community diversity. Soil Fe concentration, EC and pH are the dominant environmental factors affecting soil bacterial community composition. The important role of Fe concentration in shaping bacterial community composition is a new discovery among the similar studies. Copyright © 2018. Published by

Microbial Response to Soil Liming of Damaged Ecosystems Revealed by Pyrosequencing and Phospholipid Fatty Acid Analyses

PubMed Central

Narendrula-Kotha, Ramya; Nkongolo, Kabwe K.

2017-01-01

Aims To assess the effects of dolomitic limestone applications on soil microbial communities’ dynamics and bacterial and fungal biomass, relative abundance, and diversity in metal reclaimed regions. Methods and Results The study was conducted in reclaimed mining sites and metal uncontaminated areas. The limestone applications were performed over 35 years ago. Total microbial biomass was determined by Phospholipid fatty acids. Bacterial and fungal relative abundance and diversity were assessed using 454 pyrosequencing. There was a significant increase of total microbial biomass in limed sites (342 ng/g) compared to unlimed areas (149 ng/g). Chao1 estimates followed the same trend. But the total number of OTUs (Operational Taxonomic Units) in limed (463 OTUs) and unlimed (473 OTUs) soil samples for bacteria were similar. For fungi, OTUs were 96 and 81 for limed and unlimed soil samples, respectively. Likewise, Simpson and Shannon diversity indices revealed no significant differences between limed and unlimed sites. Bacterial and fungal groups specific to either limed or unlimed sites were identified. Five major bacterial phyla including Actinobacteria, Acidobacteria, Chloroflexi, Firmicutes, and Proteobacteria were found. The latter was the most prevalent phylum in all the samples with a relative abundance of 50%. Bradyrhizobiaceae family with 12 genera including the nitrogen fixing Bradirhizobium genus was more abundant in limed sites compared to unlimed areas. For fungi, Ascomycota was the most predominant phylum in unlimed soils (46%) while Basidiomycota phylum represented 86% of all fungi in the limed areas. Conclusion Detailed analysis of the data revealed that although soil liming increases significantly the amount of microbial biomass, the level of species diversity remain statistically unchanged even though the microbial compositions of the damaged and restored sites are different. Significance and Impact of the study Soil liming still have a significant

Bacterial endophyte communities in the foliage of coast redwood and giant sequoia.

PubMed

Carrell, Alyssa A; Frank, Anna C

2015-01-01

The endophytic bacterial microbiome, with an emerging role in plant nutrient acquisition and stress tolerance, is much less studied in natural plant populations than in agricultural crops. In a previous study, we found consistent associations between trees in the pine family and acetic acid bacteria (AAB) occurring at high relative abundance inside their needles. Our objective here was to determine if that pattern may be general to conifers, or alternatively, is more likely restricted to pines or conifers growing in nutrient limited and exposed environments. We used 16S rRNA pyrosequencing to characterize the foliar endophyte communities of two conifers in the Cupressaceae family: Two coast redwood (CR; Sequoia sempervirens) populations and one giant sequoia (GS; Sequoiadendron giganteum) population were sampled. Similar to the pines, the endophyte communities of the giant trees were dominated by Proteobacteria, Firmicutes, Acidobacteria, and Actinobacteria. However, although some major operational taxonomic units (OTUs) occurred at a high relative abundance of 10-40% in multiple samples, no specific group of bacteria dominated the endophyte community to the extent previously observed in high-elevation pines. Several of the dominating bacterial groups in the CR and GS foliage (e.g., Bacillus, Burkholderia, Actinomycetes) are known for disease- and pest suppression, raising the possibility that the endophytic microbiome protects the giant trees against biotic stress. Many of the most common and abundant OTUs in our dataset were most similar to 16S rRNA sequences from bacteria found in lichens or arctic plants. For example, an OTU belonging to the uncultured Rhizobiales LAR1 lineage, which is commonly associated with lichens, was observed at high relative abundance in many of the CR samples. The taxa shared between the giant trees, arctic plants, and lichens may be part of a broadly defined endophyte microbiome common to temperate, boreal, and tundra ecosystems.

Bacterial endophyte communities in the foliage of coast redwood and giant sequoia

PubMed Central

Carrell, Alyssa A.; Frank, Anna C.

2015-01-01

The endophytic bacterial microbiome, with an emerging role in plant nutrient acquisition and stress tolerance, is much less studied in natural plant populations than in agricultural crops. In a previous study, we found consistent associations between trees in the pine family and acetic acid bacteria (AAB) occurring at high relative abundance inside their needles. Our objective here was to determine if that pattern may be general to conifers, or alternatively, is more likely restricted to pines or conifers growing in nutrient limited and exposed environments. We used 16S rRNA pyrosequencing to characterize the foliar endophyte communities of two conifers in the Cupressaceae family: Two coast redwood (CR; Sequoia sempervirens) populations and one giant sequoia (GS; Sequoiadendron giganteum) population were sampled. Similar to the pines, the endophyte communities of the giant trees were dominated by Proteobacteria, Firmicutes, Acidobacteria, and Actinobacteria. However, although some major operational taxonomic units (OTUs) occurred at a high relative abundance of 10–40% in multiple samples, no specific group of bacteria dominated the endophyte community to the extent previously observed in high-elevation pines. Several of the dominating bacterial groups in the CR and GS foliage (e.g., Bacillus, Burkholderia, Actinomycetes) are known for disease- and pest suppression, raising the possibility that the endophytic microbiome protects the giant trees against biotic stress. Many of the most common and abundant OTUs in our dataset were most similar to 16S rRNA sequences from bacteria found in lichens or arctic plants. For example, an OTU belonging to the uncultured Rhizobiales LAR1 lineage, which is commonly associated with lichens, was observed at high relative abundance in many of the CR samples. The taxa shared between the giant trees, arctic plants, and lichens may be part of a broadly defined endophyte microbiome common to temperate, boreal, and tundra ecosystems

Microbial Diversity in Hummock and Hollow Soils of Three Wetlands on the Qinghai-Tibetan Plateau Revealed by 16S rRNA Pyrosequencing

PubMed Central

Deng, Yongcui; Cui, Xiaoyong; Hernández, Marcela; Dumont, Marc G.

2014-01-01

The wetlands of the Qinghai-Tibetan Plateau are believed to play an important role in global nutrient cycling, but the composition and diversity of microorganisms in this ecosystem are poorly characterized. An understanding of the effects of geography and microtopography on microbial populations will provide clues to the underlying mechanisms that structure microbial communities. In this study, we used pyrosequencing-based analysis of 16S rRNA gene sequences to assess and compare the composition of soil microbial communities present in hummock and hollow soils from three wetlands (Dangxiong, Hongyuan and Maduo) on the Qinghai-Tibetan Plateau, the world’s highest plateau. A total of 36 bacterial phyla were detected. Proteobacteria (34.5% average relative abundance), Actinobacteria (17.3%) and Bacteroidetes (11%) had the highest relative abundances across all sites. Chloroflexi, Acidobacteria, Verrucomicrobia, Firmicutes, and Planctomycetes were also relatively abundant (1–10%). In addition, archaeal sequences belonging to Euryarchaea, Crenarchaea and Thaumarchaea were detected. Alphaproteobacteria sequences, especially of the order Rhodospirillales, were significantly more abundant in Maduo than Hongyuan and Dangxiong wetlands. Compared with Hongyuan soils, Dangxiong and Maduo had significantly higher relative abundances of Gammaproteobacteria sequences (mainly order Xanthomonadales). Hongyuan wetland had a relatively high abundance of methanogens (mainly genera Methanobacterium, Methanosarcina and Methanosaeta) and methanotrophs (mainly Methylocystis) compared with the other two wetlands. Principal coordinate analysis (PCoA) indicated that the microbial community structure differed between locations and microtopographies and canonical correspondence analysis indicated an association between microbial community structure and soil properties or geography. These insights into the microbial community structure and the main controlling factors in wetlands of the

Impervious Surfaces Alter Soil Bacterial Communities in Urban Areas: A Case Study in Beijing, China

PubMed Central

Hu, Yinhong; Dou, Xiaolin; Li, Juanyong; Li, Feng

2018-01-01

The rapid expansion of urbanization has caused land cover change, especially the increasing area of impervious surfaces. Such alterations have significant effects on the soil ecosystem by impeding the exchange of gasses, water, and materials between soil and the atmosphere. It is unclear whether impervious surfaces have any effects on soil bacterial diversity and community composition. In the present study, we conducted an investigation of bacterial communities across five typical land cover types, including impervious surfaces (concrete), permeable pavement (bricks with round holes), shrub coverage (Buxus megistophylla Levl.), lawns (Festuca elata Keng ex E. Alexeev), and roadside trees (Sophora japonica Linn.) in Beijing, to explore the response of bacteria to impervious surfaces. The soil bacterial communities were addressed by high-throughput sequencing of the bacterial 16S rRNA gene. We found that Proteobacteria, Actinobacteria, Acidobacteria, Bacteroidetes, Chloroflexi, and Firmicutes were the predominant phyla in urban soils. Soil from impervious surfaces presented a lower bacterial diversity, and differed greatly from other types of land cover. Soil bacterial diversity was predominantly affected by Zn, dissolved organic carbon (DOC), and soil moisture content (SMC). The composition of the bacterial community was similar under shrub coverage, roadside trees, and lawns, but different from beneath impervious surfaces and permeable pavement. Variance partitioning analysis showed that edaphic properties contributed to 12% of the bacterial community variation, heavy metal pollution explained 3.6% of the variation, and interaction between the two explained 33% of the variance. Together, our data indicate that impervious surfaces induced changes in bacterial community composition and decrease of bacterial diversity. Interactions between edaphic properties and heavy metals were here found to change the composition of the bacterial community and diversity across

Bacterial endophyte communities in the foliage of coast redwood and giant sequoia

DOE Office of Scientific and Technical Information (OSTI.GOV)

Carrell, Alyssa A.; Frank, Anna C.

The endophytic bacterial microbiome, with an emerging role in plant nutrient acquisition and stress tolerance, is much less studied in natural plant populations than in agricultural crops. In a previous study, we found consistent associations between trees in the pine family and acetic acid bacteria (AAB) occurring at high relative abundance inside their needles. Our objective here was to determine if that pattern may be general to conifers, or alternatively, is more likely restricted to pines or conifers growing in nutrient limited and exposed environments. We used 16S rRNA pyrosequencing to characterize the foliar endophyte communities of two conifers inmore » the Cupressaceae family: Two coast redwood (CR; Sequoia sempervirens) populations and one giant sequoia (GS; Sequoiadendron giganteum) population were sampled. Similar to the pines, the endophyte communities of the giant trees were dominated by Proteobacteria, Firmicutes, Acidobacteria, and Actinobacteria. However, although some major operational taxonomic units (OTUs) occurred at a high relative abundance of 10–40% in multiple samples, no specific group of bacteria dominated the endophyte community to the extent previously observed in high-elevation pines. Several of the dominating bacterial groups in the CR and GS foliage (e.g., Bacillus, Burkholderia, Actinomycetes) are known for disease- and pest suppression, raising the possibility that the endophytic microbiome protects the giant trees against biotic stress. Many of the most common and abundant OTUs in our dataset were most similar to 16S rRNA sequences from bacteria found in lichens or arctic plants. For example, an OTU belonging to the uncultured Rhizobiales LAR1 lineage, which is commonly associated with lichens, was observed at high relative abundance in many of the CR samples. Lastly, the taxa shared between the giant trees, arctic plants, and lichens may be part of a broadly defined endophyte microbiome common to temperate, boreal, and

Bacterial endophyte communities in the foliage of coast redwood and giant sequoia

DOE PAGES

Carrell, Alyssa A.; Frank, Anna C.

2015-09-22

The endophytic bacterial microbiome, with an emerging role in plant nutrient acquisition and stress tolerance, is much less studied in natural plant populations than in agricultural crops. In a previous study, we found consistent associations between trees in the pine family and acetic acid bacteria (AAB) occurring at high relative abundance inside their needles. Our objective here was to determine if that pattern may be general to conifers, or alternatively, is more likely restricted to pines or conifers growing in nutrient limited and exposed environments. We used 16S rRNA pyrosequencing to characterize the foliar endophyte communities of two conifers inmore » the Cupressaceae family: Two coast redwood (CR; Sequoia sempervirens) populations and one giant sequoia (GS; Sequoiadendron giganteum) population were sampled. Similar to the pines, the endophyte communities of the giant trees were dominated by Proteobacteria, Firmicutes, Acidobacteria, and Actinobacteria. However, although some major operational taxonomic units (OTUs) occurred at a high relative abundance of 10–40% in multiple samples, no specific group of bacteria dominated the endophyte community to the extent previously observed in high-elevation pines. Several of the dominating bacterial groups in the CR and GS foliage (e.g., Bacillus, Burkholderia, Actinomycetes) are known for disease- and pest suppression, raising the possibility that the endophytic microbiome protects the giant trees against biotic stress. Many of the most common and abundant OTUs in our dataset were most similar to 16S rRNA sequences from bacteria found in lichens or arctic plants. For example, an OTU belonging to the uncultured Rhizobiales LAR1 lineage, which is commonly associated with lichens, was observed at high relative abundance in many of the CR samples. Lastly, the taxa shared between the giant trees, arctic plants, and lichens may be part of a broadly defined endophyte microbiome common to temperate, boreal, and

Temporal and Spatial Impact of Human Cadaver Decomposition on Soil Bacterial and Arthropod Community Structure and Function

PubMed Central

Singh, Baneshwar; Minick, Kevan J.; Strickland, Michael S.; Wickings, Kyle G.; Crippen, Tawni L.; Tarone, Aaron M.; Benbow, M. Eric; Sufrin, Ness; Tomberlin, Jeffery K.; Pechal, Jennifer L.

2018-01-01

As vertebrate carrion decomposes, there is a release of nutrient-rich fluids into the underlying soil, which can impact associated biological community structure and function. How these changes alter soil biogeochemical cycles is relatively unknown and may prove useful in the identification of carrion decomposition islands that have long lasting, focal ecological effects. This study investigated the spatial (0, 1, and 5 m) and temporal (3–732 days) dynamics of human cadaver decomposition on soil bacterial and arthropod community structure and microbial function. We observed strong evidence of a predictable response to cadaver decomposition that varies over space for soil bacterial and arthropod community structure, carbon (C) mineralization and microbial substrate utilization patterns. In the presence of a cadaver (i.e., 0 m samples), the relative abundance of Bacteroidetes and Firmicutes was greater, while the relative abundance of Acidobacteria, Chloroflexi, Gemmatimonadetes, and Verrucomicrobia was lower when compared to samples at 1 and 5 m. Micro-arthropods were more abundant (15 to 17-fold) in soils collected at 0 m compared to either 1 or 5 m, but overall, micro-arthropod community composition was unrelated to either bacterial community composition or function. Bacterial community structure and microbial function also exhibited temporal relationships, whereas arthropod community structure did not. Cumulative precipitation was more effective in predicting temporal variations in bacterial abundance and microbial activity than accumulated degree days. In the presence of the cadaver (i.e., 0 m samples), the relative abundance of Actinobacteria increased significantly with cumulative precipitation. Furthermore, soil bacterial communities and C mineralization were sensitive to the introduction of human cadavers as they diverged from baseline levels and did not recover completely in approximately 2 years. These data are valuable for understanding ecosystem

The abundance of functional genes, cbbL, nifH, amoA and apsA, and bacterial community structure of intertidal soil from Arabian Sea.

PubMed

Keshri, Jitendra; Yousuf, Basit; Mishra, Avinash; Jha, Bhavanath

2015-06-01

The Gulf of Cambay is a trumpet-shaped inlet of the Arabian Sea, located along the west coast of India and confronts a high tidal range with strong water currents. The region belongs to a semi-arid zone and saline alkaline intertidal soils are considered biologically extreme. The selected four soil types (S1-S4) were affected by salinity, alkalinity and sodicity. Soil salinity ranged from 20 to 126 dS/m, soil pH 8.6-10.0 with high sodium adsorption ratio (SAR) and exchangeable sodium percentage (ESP). Abundance of the key functional genes like cbbL, nifH, amoA and apsA involved in biogeochemical cycling were targeted using qPCR, which varied from (2.36 ± 0.03) × 10(4) to (2.87 ± 0.26) × 10(8), (1.18 ± 0.28) × 10(6) to (1.01 ± 0.26) × 10(9), (1.41 ± 0.21) × 10(6) to (1.29 ± 0.05) × 10(8) and (8.47 ± 0.23) × 10(4) to (1.73 ± 0.01) × 10(6) per gram dry weight, respectively. The microbial community structure revealed that soils S1 and S3 were dominated by phylum Firmicutes whereas S4 and S2 showed an abundance of Proteobacterial clones. These soils also represented Bacteroidetes, Chloroflexi, Actinobacteria, Planctomycetes and Acidobacteria clones. Molecular phylogeny showed a significant variation in the bacterial community distribution among the intertidal soil types. A high number of novel taxonomic units were observed which makes the intertidal zone a unique reservoir of unidentified bacterial taxa that may be explored further. Copyright © 2015 Elsevier GmbH. All rights reserved.

Bacterial diversity and community along the succession of biological soil crusts in the Gurbantunggut Desert, Northern China.

PubMed

Zhang, Bingchang; Kong, Weidong; Wu, Nan; Zhang, Yuanming

2016-06-01

Biological soil crusts (BSCs) are common and play critical roles in semi-arid and arid ecosystems. Bacteria, as an important community in BSCs, play critical roles in biochemical processes. However, how bacterial diversity and community change in different successional stages of BSCs is still unknown. We used 454 pyrosequencing of 16S rRNA to investigate the bacterial composition and community, and the relationships between bacterial composition and environmental factors were also explored. In different successional stages of BSCs, the number of bacteria operational taxonomic units (OTUs) detected in each sample ranged from 2572 to 3157. Proteobacteria, Cyanobacteria, Bacteroidetes were dominant in BSCs, followed by Firmicutes, Acidobacteria, and Actinobacteria. At the successional stages of BSCs, bacterial communities, OTU composition and their relative abundance notably differentiated, and Cyanobacteria, especially Microcoleus vaginatus, dominated algal crust and lichen crust, and were the main C-fixing bacteria in BSCs. Proteobacteria and Bacteroidetes increased with the development of BSCs. OTUs related to Planomicrobium Chinese, Desulfobulbus sp., Desulfomicrobium sp., Arthrobacter sp., and Ahhaerbacter sp. showed higher relative abundance in bare sand than other successional stages of BSCs, while relative abundance of Sphingomonas sp. Niastella sp., Pedobacter, Candidatus solobacter, and Streptophyta increased with the development of BSCs. In successional stages of BSCs, bacterial OTUs composition demonstrated strong correlations with soil nutrients, soil salts, and soil enzymes. Additionally, variation of bacterial composition led to different ecological function. In bare sand, some species were related with mineral metabolism or promoting plant growth, and in algal crust and lichen crust, C-fixing bacteria increased and accumulated C to the desert soil. In later developed stage of BSCs, bacteria related with decomposition of organic matter, such as

Temporal and Spatial Impact of Human Cadaver Decomposition on Soil Bacterial and Arthropod Community Structure and Function.

PubMed

Singh, Baneshwar; Minick, Kevan J; Strickland, Michael S; Wickings, Kyle G; Crippen, Tawni L; Tarone, Aaron M; Benbow, M Eric; Sufrin, Ness; Tomberlin, Jeffery K; Pechal, Jennifer L

2017-01-01

As vertebrate carrion decomposes, there is a release of nutrient-rich fluids into the underlying soil, which can impact associated biological community structure and function. How these changes alter soil biogeochemical cycles is relatively unknown and may prove useful in the identification of carrion decomposition islands that have long lasting, focal ecological effects. This study investigated the spatial (0, 1, and 5 m) and temporal (3-732 days) dynamics of human cadaver decomposition on soil bacterial and arthropod community structure and microbial function. We observed strong evidence of a predictable response to cadaver decomposition that varies over space for soil bacterial and arthropod community structure, carbon (C) mineralization and microbial substrate utilization patterns. In the presence of a cadaver (i.e., 0 m samples), the relative abundance of Bacteroidetes and Firmicutes was greater, while the relative abundance of Acidobacteria, Chloroflexi, Gemmatimonadetes, and Verrucomicrobia was lower when compared to samples at 1 and 5 m. Micro-arthropods were more abundant (15 to 17-fold) in soils collected at 0 m compared to either 1 or 5 m, but overall, micro-arthropod community composition was unrelated to either bacterial community composition or function. Bacterial community structure and microbial function also exhibited temporal relationships, whereas arthropod community structure did not. Cumulative precipitation was more effective in predicting temporal variations in bacterial abundance and microbial activity than accumulated degree days. In the presence of the cadaver (i.e., 0 m samples), the relative abundance of Actinobacteria increased significantly with cumulative precipitation. Furthermore, soil bacterial communities and C mineralization were sensitive to the introduction of human cadavers as they diverged from baseline levels and did not recover completely in approximately 2 years. These data are valuable for understanding ecosystem function

Glyphosate effects on soil rhizosphere-associated bacterial communities.

PubMed

Newman, Molli M; Hoilett, Nigel; Lorenz, Nicola; Dick, Richard P; Liles, Mark R; Ramsier, Cliff; Kloepper, Joseph W

2016-02-01

Glyphosate is one of the most widely used herbicides in agriculture with predictions that 1.35 million metric tons will be used annually by 2017. With the advent of glyphosate tolerant (GT) cropping more than 10 years ago, there is now concern for non-target effects on soil microbial communities that has potential to negatively affect soil functions, plant health, and crop productivity. Although extensive research has been done on short-term response to glyphosate, relatively little information is available on long-term effects. Therefore, the overall objective was to investigate shifts in the rhizosphere bacterial community following long-term glyphosate application on GT corn and soybean in the greenhouse. In this study, rhizosphere soil was sampled from rhizoboxes following 4 growth periods, and bacterial community composition was compared between glyphosate treated and untreated rhizospheres using next-generation barcoded sequencing. In the presence or absence of glyphosate, corn and soybean rhizospheres were dominated by members of the phyla Proteobacteria, Acidobacteria, and Actinobacteria. Proteobacteria (particularly gammaproteobacteria) increased in relative abundance for both crops following glyphosate exposure, and the relative abundance of Acidobacteria decreased in response to glyphosate exposure. Given that some members of the Acidobacteria are involved in biogeochemical processes, a decrease in their abundance could lead to significant changes in nutrient status of the rhizosphere. Our results also highlight the need for applying culture-independent approaches in studying the effects of pesticides on the soil and rhizosphere microbial community. Copyright © 2015 The Authors. Published by Elsevier B.V. All rights reserved.

Surfactants tailored by the class Actinobacteria

PubMed Central

Kügler, Johannes H.; Le Roes-Hill, Marilize; Syldatk, Christoph; Hausmann, Rudolf

2015-01-01

Globally the change towards the establishment of a bio-based economy has resulted in an increased need for bio-based applications. This, in turn, has served as a driving force for the discovery and application of novel biosurfactants. The class Actinobacteria represents a vast group of microorganisms with the ability to produce a diverse range of secondary metabolites, including surfactants. Understanding the extensive nature of the biosurfactants produced by actinobacterial strains can assist in finding novel biosurfactants with new potential applications. This review therefore presents a comprehensive overview of the knowledge available on actinobacterial surfactants, the chemical structures that have been completely or partly elucidated, as well as the identity of the biosurfactant-producing strains. Producer strains of not yet elucidated compounds are discussed, as well as the original habitats of all the producer strains, which seems to indicate that biosurfactant production is environmentally driven. Methodology applied in the isolation, purification and structural elucidation of the different types of surface active compounds, as well as surfactant activity tests, are also discussed. Overall, actinobacterial surfactants can be summarized to include the dominantly occurring trehalose-comprising surfactants, other non-trehalose containing glycolipids, lipopeptides and the more rare actinobacterial surfactants. The lack of structural information on a large proportion of actinobacterial surfactants should be considered as a driving force to further explore the abundance and diversity of these compounds. This would allow for a better understanding of actinobacterial surface active compounds and their potential for biotechnological application. PMID:25852670

Sequence Analysis of Changes in Microbial Composition in Different Milk Products During Fermentation and Storage.

PubMed

Zalewska, Barbora; Kaevska, Marija; Slana, Iva

2018-02-01

The objective of this study was to analyze the changes in the microbiota of milk products during fermentation and storage. Two kinds of Yoghurt, one Kefir, and one Acidophilus milk were observed during the fermentation process and storage using 16S rDNA amplicon sequencing. Cow's, goat's, raw and pasteurized milk were also examined. The most represented organisms in all manufactured products were shown to be those of the phylum Firmicutes. In some products, Proteobacteria, Bacteroidetes and Actinobacteria were also present in high amounts.

Metagenomic analysis of bacterial and archaeal assemblages in the soil-mousse surrounding a geothermal spring.

PubMed

Bhatia, Sonu; Batra, Navneet; Pathak, Ashish; Joshi, Amit; Souza, Leila; Almeida, Paulo; Chauhan, Ashvini

2015-09-01

The soil-mousse surrounding a geothermal spring was analyzed for bacterial and archaeal diversity using 16S rRNA gene amplicon metagenomic sequencing which revealed the presence of 18 bacterial phyla distributed across 109 families and 219 genera. Firmicutes, Actinobacteria, and the Deinococcus-Thermus group were the predominant bacterial assemblages with Crenarchaeota and Thaumarchaeota as the main archaeal assemblages in this largely understudied geothermal habitat. Several metagenome sequences remained taxonomically unassigned suggesting the presence of a repertoire of hitherto undescribed microbes in this geothermal soil-mousse econiche.

Korean indigenous bacterial species with valid names belonging to the phylum Actinobacteria.

PubMed

Bae, Kyung Sook; Kim, Mi Sun; Lee, Ji Hee; Kang, Joo Won; Kim, Dae In; Lee, Ji Hee; Seong, Chi Nam

2016-12-01

To understand the isolation and classification state of actinobacterial species with valid names for Korean indigenous isolates, isolation source, regional origin, and taxonomic affiliation of the isolates were studied. At the time of this writing, the phylum Actinobacteria consisted of only one class, Actinobacteria, including five subclasses, 10 orders, 56 families, and 330 genera. Moreover, new taxa of this phylum continue to be discovered. Korean actinobacterial species with a valid name has been reported from 1995 as Tsukamurella inchonensis isolated from a clinical specimen. In 1997, Streptomyces seoulensis was validated with the isolate from the natural Korean environment. Until Feb. 2016, 256 actinobacterial species with valid names originated from Korean territory were listed on LPSN. The species were affiliated with three subclasses (Acidimicrobidae, Actinobacteridae, and Rubrobacteridae), four orders (Acidimicrobiales, Actinomycetales, Bifidobacteriales, and Solirubrobacterales), 12 suborders, 36 families, and 93 genera. Most of the species belonged to the subclass Actinobacteridae, and almost of the members of this subclass were affiliated with the order Actinomycetales. A number of novel isolates belonged to the families Nocardioidaceae, Microbacteriaceae, Intrasporangiaceae, and Streptomycetaceae as well as the genera Nocardioides, Streptomyces, and Microbacterium. Twenty-six novel genera and one novel family, Motilibacteraceae, were created first with Korean indigenous isolates. Most of the Korean indigenous actionobacterial species were isolated from natural environments such as soil, seawater, tidal flat sediment, and fresh-water. A considerable number of species were isolated from artificial resources such as fermented foods, wastewater, compost, biofilm, and water-cooling systems or clinical specimens. Korean indigenous actinobacterial species were isolated from whole territory of Korea, and especially a large number of species were from Jeju

Electricity generation from cattle dung using microbial fuel cell technology during anaerobic acidogenesis and the development of microbial populations.

PubMed

Zhao, Guang; Ma, Fang; Wei, Li; Chua, Hong; Chang, Chein-Chi; Zhang, Xiao-Jun

2012-09-01

A microbial fuel cell (MFC) was constructed to investigate the possible generation of electricity using cattle dung as a substrate. After 30 days of operation, stable electricity was generated, and the maximum volumetric power density was 0.220 W/m(3). The total chemical oxygen demand (TCOD) removal and coulombic efficiency (CE) of the MFC reached 73.9±1.8% and 2.79±0.6%, respectively, after 120 days of operation. Acetate was the main metabolite in the anolyte, and other volatile fatty acids (VFAs) (propionate and butyrate) were present in minor amounts. The PCR-DGGE analysis indicated that the following five groups of microbes were present: Proteobacteria, Bacteroides, Chloroflexi, Actinobacteria and Firmicutes. Proteobacteria and Firmicutes were the dominant phyla in the sample; specifically, 36.3% and 24.2% of the sequences obtained were Proteobacteria and Firmicutes, respectively. Clostridium sp., Pseudomonas luteola and Ochrobactrum pseudogrignonense were the most dominant groups during the electricity generation process. The diversity of archaea dramatically decreased after 20 days of operation. The detected archaea were hydrogenotrophic methanogens, and the Methanobacterium genus disappeared during the periods of stable electricity generation via acidogenesis. Copyright © 2012 Elsevier Ltd. All rights reserved.

Unravelling the microbiome of eggs of the endangered sea turtle Eretmochelys imbricata identifies bacteria with activity against the emerging pathogen Fusarium falciforme.

PubMed

Sarmiento-Ramírez, Jullie M; van der Voort, Menno; Raaijmakers, Jos M; Diéguez-Uribeondo, Javier

2014-01-01

Habitat bioaugmentation and introduction of protective microbiota have been proposed as potential conservation strategies to rescue endangered mammals and amphibians from emerging diseases. For both strategies, insight into the microbiomes of the endangered species and their habitats is essential. Here, we sampled nests of the endangered sea turtle species Eretmochelys imbricata that were infected with the fungal pathogen Fusarium falciforme. Metagenomic analysis of the bacterial communities associated with the shells of the sea turtle eggs revealed approximately 16,664 operational taxonomic units, with Proteobacteria, Actinobacteria, Firmicutes and Bacteroidetes as the most dominant phyla. Subsequent isolation of Actinobacteria from the eggshells led to the identification of several genera (Streptomyces, Amycolaptosis, Micromomospora Plantactinospora and Solwaraspora) that inhibit hyphal growth of the pathogen F. falciforme. These bacterial genera constitute a first set of microbial indicators to evaluate the potential role of microbiota in conservation of endangered sea turtle species.

Butyrate production in phylogenetically diverse Firmicutes isolated from the chicken caecum

PubMed Central

Eeckhaut, Venessa; Van Immerseel, Filip; Croubels, Siska; De Baere, Siegrid; Haesebrouck, Freddy; Ducatelle, Richard; Louis, Petra; Vandamme, Peter

2011-01-01

Summary Sixteen butyrate‐producing bacteria were isolated from the caecal content of chickens and analysed phylogenetically. They did not represent a coherent phylogenetic group, but were allied to four different lineages in the Firmicutes phylum. Fourteen strains appeared to represent novel species, based on a level of ≤ 98.5% 16S rRNA gene sequence similarity towards their nearest validly named neighbours. The highest butyrate concentrations were produced by the strains belonging to clostridial clusters IV and XIVa, clusters which are predominant in the chicken caecal microbiota. In only one of the 16 strains tested, the butyrate kinase operon could be amplified, while the butyryl‐CoA : acetate CoA‐transferase gene was detected in eight strains belonging to clostridial clusters IV, XIVa and XIVb. None of the clostridial cluster XVI isolates carried this gene based on degenerate PCR analyses. However, another CoA‐transferase gene more similar to propionate CoA‐transferase was detected in the majority of the clostridial cluster XVI isolates. Since this gene is located directly downstream of the remaining butyrate pathway genes in several human cluster XVI bacteria, it may be involved in butyrate formation in these bacteria. The present study indicates that butyrate producers related to cluster XVI may play a more important role in the chicken gut than in the human gut. PMID:21375722

Quorum quenching properties of Actinobacteria isolated from Malaysian tropical soils.

PubMed

Devaraj, Kavimalar; Tan, Geok Yuan Annie; Chan, Kok-Gan

2017-08-01

In this study, a total of 147 soil actinobacterial strains were screened for their ability to inhibit response of Chromobacterium violaceum CV026 to short chain N-acyl homoserine lactone (AHL) which is a quorum sensing molecule. Of these, three actinobacterial strains showed positive for violacein inhibition. We further tested these strains for the inhibition of Pseudomonas aeruginosa PAO1 quorum sensing-regulated phenotypes, namely, swarming and pyocyanin production. The three strains were found to inhibit at least one of the quorum sensing-regulated phenotypes of PAO1. Phylogenetic analysis of the 16S rRNA gene sequences indicated that these strains belong to the genera Micromonospora, Rhodococcus and Streptomyces. This is the first report presenting quorum quenching activity by a species of the genus Micromonospora. Our data suggest that Actinobacteria may be a rich source of active compounds that can act against bacterial quorum sensing system.

Metagenomic analysis of bacterial and archaeal assemblages in the soil-mousse surrounding a geothermal spring

PubMed Central

Bhatia, Sonu; Batra, Navneet; Pathak, Ashish; Joshi, Amit; Souza, Leila; Almeida, Paulo; Chauhan, Ashvini

2015-01-01

The soil-mousse surrounding a geothermal spring was analyzed for bacterial and archaeal diversity using 16S rRNA gene amplicon metagenomic sequencing which revealed the presence of 18 bacterial phyla distributed across 109 families and 219 genera. Firmicutes, Actinobacteria, and the Deinococcus-Thermus group were the predominant bacterial assemblages with Crenarchaeota and Thaumarchaeota as the main archaeal assemblages in this largely understudied geothermal habitat. Several metagenome sequences remained taxonomically unassigned suggesting the presence of a repertoire of hitherto undescribed microbes in this geothermal soil-mousse econiche. PMID:26484255

Diversity and homogeneity of oral microbiota in healthy Korean pre-school children using pyrosequencing.

PubMed

Lee, Soo Eon; Nam, Ok Hyung; Lee, Hyo-Seol; Choi, Sung Chul

2016-07-01

Objectives The purpose of this study was designed to identify the oral microbiota in healthy Korean pre-school children using pyrosequencing. Materials and methods Dental plaque samples were obtained form 10 caries-free pre-school children. The samples were analysed using pyrosequencing. Results The pyrosequencing analysis revealed that, at the phylum level, Proteobacteria, Firmicutes, Bacteroidetes, Actinobacteria and Fusobacteria showed high abundance. Also, predominant genera were identified as core microbiome, such as Streptococcus, Neisseria, Capnocytophaga, Haemophilus and Veilonella. Conclusions The diversity and homogeneity was shown in the dental plaque microbiota in healthy Korean pre-school children.

Environmental monitoring and assessment of antibacterial metabolite producing actinobacteria screened from marine sediments in south coastal regions of Karnataka, India.

PubMed

Skariyachan, Sinosh; Garka, Shruthi; Puttaswamy, Sushmitha; Shanbhogue, Shobitha; Devaraju, Raksha; Narayanappa, Rajeswari

2017-06-01

Assessment of the therapeutic potential of secondary metabolite producing microorganisms from the marine coastal areas imparts scope and application in the field of environmental monitoring. The present study aims to screen metabolites with antibacterial potential from actionbacteria associated with marine sediments collected from south coastal regions of Karnataka, India. The actinobacteria were isolated and characterized from marine sediments by standard protocol. The metabolites were extracted, and antibacterial potential was analyzed against eight hospital associated bacteria. The selected metabolites were partially characterized by proximate analysis, SDS-PAGE, and FTIR-spectroscopy. The antibiogram of the test clinical isolates revealed that they were emerged as multidrug-resistant strains (P ≤ 0.05). Among six actinobacteria (IS1-1S6) screened, 100 μl -1 metabolite from IS1 showed significant antibacterial activities against all the clinical isolates except Pseudomonas aeruginosa. IS2 demonstrated antimicrobial potential towards Proteus mirabilis, Streptococcus pyogenes, and Escherichia coli. The metabolite from IS3 showed activity against Strep. pyogenes and E. coli. The metabolites from IS4, IS5, and IS6 exhibited antimicrobial activities against Ps. aeruginosa (P ≤ 0.05). The two metabolites that depicted highest antibacterial activities against the test strains were suggested to be antimicrobial peptides with low molecular weight. These isolates were characterized and designated as Streptomyces sp. strain mangaluru01 and Streptomyces sp. mangaloreK01 by 16S ribosomal DNA (rDNA) sequencing. This study suggests that south coastal regions of Karnataka, India, are one of the richest sources of antibacterial metabolites producing actinobacteria and monitoring of these regions for therapeutic intervention plays profound role in healthcare management.

Determinants of bacterial communities in Canadian agroforestry systems.

PubMed

Banerjee, Samiran; Baah-Acheamfour, Mark; Carlyle, Cameron N; Bissett, Andrew; Richardson, Alan E; Siddique, Tariq; Bork, Edward W; Chang, Scott X

2016-06-01

Land-use change is one of the most important factors influencing soil microbial communities, which play a pivotal role in most biogeochemical and ecological processes. Using agroforestry systems as a model, this study examined the effects of land uses and edaphic properties on bacterial communities in three agroforestry types covering a 270 km soil-climate gradient in Alberta, Canada. Our results demonstrate that land-use patterns exert stronger effects on soil bacterial communities than soil zones in these agroforestry systems. Plots with trees in agroforestry systems promoted greater bacterial abundance and to some extent species richness, which was associated with more nutrient-rich soil resources. While Acidobacteria, Actinobacteria and Alphaproteobacteria were the dominant bacterial phyla and subphyla across land uses, Arthrobacter, Acidobacteria_Gp16, Burkholderia, Rhodanobacter and Rhizobium were the keystone taxa in these agroforestry systems. Soil pH and carbon contents emerged as the major determinants of bacterial community characteristics. We found non-random co-occurrence and modular patterns of soil bacterial communities, and these patterns were controlled by edaphic factors and not their taxonomy. Overall, this study highlights the drivers and co-occurrence patterns of soil microbial communities in agroforestry systems. © 2015 Society for Applied Microbiology and John Wiley & Sons Ltd.

Comparative single-cell genomics reveals potential ecological niches for the freshwater acI Actinobacteria lineage.

PubMed

Ghylin, Trevor W; Garcia, Sarahi L; Moya, Francisco; Oyserman, Ben O; Schwientek, Patrick; Forest, Katrina T; Mutschler, James; Dwulit-Smith, Jeffrey; Chan, Leong-Keat; Martinez-Garcia, Manuel; Sczyrba, Alexander; Stepanauskas, Ramunas; Grossart, Hans-Peter; Woyke, Tanja; Warnecke, Falk; Malmstrom, Rex; Bertilsson, Stefan; McMahon, Katherine D

2014-12-01

Members of the acI lineage of Actinobacteria are the most abundant microorganisms in most freshwater lakes; however, our understanding of the keys to their success and their role in carbon and nutrient cycling in freshwater systems has been hampered by the lack of pure cultures and genomes. We obtained draft genome assemblies from 11 single cells representing three acI tribes (acI-A1, acI-A7, acI-B1) from four temperate lakes in the United States and Europe. Comparative analysis of acI SAGs and other available freshwater bacterial genomes showed that acI has more gene content directed toward carbohydrate acquisition as compared to Polynucleobacter and LD12 Alphaproteobacteria, which seem to specialize more on carboxylic acids. The acI genomes contain actinorhodopsin as well as some genes involved in anaplerotic carbon fixation indicating the capacity to supplement their known heterotrophic lifestyle. Genome-level differences between the acI-A and acI-B clades suggest specialization at the clade level for carbon substrate acquisition. Overall, the acI genomes appear to be highly streamlined versions of Actinobacteria that include some genes allowing it to take advantage of sunlight and N-rich organic compounds such as polyamines, di- and oligopeptides, branched-chain amino acids and cyanophycin. This work significantly expands the known metabolic potential of the cosmopolitan freshwater acI lineage and its ecological and genetic traits.

Organic loading rate and hydraulic retention time shape distinct ecological networks of anaerobic digestion related microbiome.

PubMed

Xu, Rui; Yang, Zhao-Hui; Zheng, Yue; Liu, Jian-Bo; Xiong, Wei-Ping; Zhang, Yan-Ru; Lu, Yue; Xue, Wen-Jing; Fan, Chang-Zheng

2018-04-22

Understanding of how anaerobic digestion (AD)-related microbiomes are constructed by operational parameters or their interactions within the biochemical process is limited. Using high-throughput sequencing and molecular ecological network analysis, this study shows the succession of AD-related microbiome hosting diverse members of the phylum Actinobacteria, Bacteroidetes, Euryarchaeota, and Firmicutes, which were affected by organic loading rate (OLR) and hydraulic retention time (HRT). OLR formed finer microbial network modules than HRT (12 vs. 6), suggesting the further subdivision of functional components. Biomarkers were also identified in OLR or HRT groups (e.g. the family Actinomycetaceae, Methanosaetaceae and Aminiphilaceae). The most pair-wise link between Firmicutes and biogas production indicates the keystone members based on network features can be considered as markers in the regulation of AD. A set of 40% species ("core microbiome") were similar across different digesters. Such noteworthy overlap of microbiomes indicates they are generalists in maintaining the ecological stability of digesters. Copyright © 2018 Elsevier Ltd. All rights reserved.

Dynamics of the oral microbiota as a tool to estimate time since death.

PubMed

Adserias-Garriga, J; Quijada, N M; Hernandez, M; Rodríguez Lázaro, D; Steadman, D; Garcia-Gil, L J

2017-06-27

The oral cavity harbors one of the most diverse microbiomes in the human body. It has been shown to be the second most complex in the body after the gastrointestinal tract. Upon death, the indigenous microorganisms lead to the decomposition of the carcass. Therefore, the oral cavity and gastrointestinal tract microbiomes play a key role in human decomposition. The aim of the present study is to monitor the microbiome of decaying bodies on a daily basis and to identify signature bacterial taxa, that can improve postmortem interval estimation. Three individuals (one male and two female) donated to the University of Tennessee Forensic Anthropology Center for the W.M. Bass Donated Skeletal Collection were studied. Oral swab samples were taken daily throughout the different stages of cadaveric putrefaction. DNA was extracted and analyzed by next-generation sequencing techniques. The three cadavers showed similar overall successional changes during the decomposition process. Firmicutes and Actinobacteria are the predominant phyla in the fresh stage. The presence of Tenericutes corresponds to bloat stage. Firmicutes is the predominant phylum in advanced decay, but the Firmicutes community is a different one from the predominant Firmicutes of the fresh stage. This study depicts the thanatomicrobiome successional changes in the oral cavity, and highlights its potential use in forensic cases as a quantitative and objective approach to estimate postmortem interval, from an ecological rationale. © 2017 John Wiley & Sons A/S. Published by John Wiley & Sons Ltd.

Spatiotemporal changes in bacterial community and microbial activity in a full-scale drinking water treatment plant.

PubMed

Hou, Luanfeng; Zhou, Qin; Wu, Qingping; Gu, Qihui; Sun, Ming; Zhang, Jumei

2018-06-01

To gain insight into the bacterial dynamics present in drinking water treatment (DWT) systems, the microbial community and activity in a full-scale DWT plant (DWTP) in Guangzhou, South China, were investigated using Illumina Hiseq sequencing analyses combined with cultivation-based techniques during the wet and dry seasons. Illumina sequencing analysis of 16S rRNA genes revealed a large shift in the proportion of Actinobacteria, Proteobacteria and Firmicutes during the treatment process, with the proportion of Actinobacteria decreased sharply, whereas that of Proteobacteria and Firmicutes increased and predominated in treated water. Both microbial activity and bacterial diversity during the treatment process showed obvious spatial variation, with higher levels observed during the dry season and lower levels during the wet season. Clustering analysis and principal component analysis indicated dramatic shifts in the bacterial community after chlorination, suggesting that chlorination was highly effective at influencing the bacterial community. The bacterial community structure of finished water primarily comprised Pseudomonas, Citrobacter, and Acinetobacter, and interestingly showed high similarity to biofilms on granular activated carbon. Additionally, the abundance of bacterial communities was relatively stable in finished water and did not change with the season. A large number of unique operational taxonomic units were shared during treatment steps, indicating the presence of a diverse core microbiome throughout the treatment process. Opportunistic pathogens, including Pseudomonas, Acinetobacter, Citrobacter, Mycobacterium, Salmonella, Staphylococcus, Legionella, Streptococcus and Enterococcus, were detected in water including finished water, suggesting a potential threat to drinking-water safety. We also detected bacteria isolated from each treatment step using the pure-culture method. In particular, two isolates, identified as Mycobacterium sp. and Blastococcus

Unicellular cyanobacteria Synechocystis accommodate heterotrophic bacteria with varied enzymatic and metal resistance properties.

PubMed

Abdulaziz, Anas; Sageer, Saliha; Chekidhenkuzhiyil, Jasmin; Vijayan, Vijitha; Pavanan, Pratheesh; Athiyanathil, Sujith; Nair, Shanta

2016-08-01

The interactions between heterotrophic bacteria and primary producers have a profound impact on the functioning of marine ecosystem. We characterized the enzymatic and metal resistance properties of fourteen heterotrophic bacteria isolated from a unicellular cyanobacterium Synechocystis sp. that came from a heavy metal contaminated region of Cochin estuary, southwest coast of India. Based on 16S rRNA gene sequence similarities, the heterotrophic bacteria were grouped into three phyla: namely Actinobacteria, Firmicute, and Proteobacteria. Overall Proteobacteria showed a higher level of enzyme expression while Actinobacteria and Firmicutes showed higher tolerance to heavy metals. Among Proteobacteria, an isolate of Marinobacter hydrocarbonoclasticus (MMRF-584) showed highest activities of β-glucosidase (1.58 ± 0.2 μMml(-1)  min(-1) ) and laminarinase (1170.17 ± 95.4 μgml(-1)  min(-1) ), while other two isolates of M. hydrocarbonoclasticus, MMRF-578 and 581, showed highest phosphatase (44.71 ± 0.2 μMml(-1)  min(-1) ) and aminopeptidase (33.22 ± 0 μMml(-1)  min(-1) ) activities respectively. Among Firmicutes, the Virgibacillus sp. MMRF-571 showed exceptional resistance against the toxic heavy metals Cd (180 mM), Pb (150 mM), and Hg (0.5 mM). Bacillus cereus, MMRF-575, showed resistance to the highest concentrations of Co (250 mM), Cd (150 mM), Pb (180 mM), Hg (0.5 mM), Ni (280 mM), and Zn (250 mM) tested. Our results show that heterotrophic bacteria with varied enzymatic and metal resistance properties are associated with Synechocystis sp. Further studies to delineate the role of these heterotrophic bacteria in protecting primary producers from toxic effects of heavy metals and their potential application in bioremediation will be appreciated. © 2016 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

454 pyrosequencing analysis on faecal samples from a randomized DBPC trial of colicky infants treated with Lactobacillus reuteri DSM 17938.

PubMed

Roos, Stefan; Dicksved, Johan; Tarasco, Valentina; Locatelli, Emanuela; Ricceri, Fulvio; Grandin, Ulf; Savino, Francesco

2013-01-01

To analyze the global microbial composition, using large-scale DNA sequencing of 16 S rRNA genes, in faecal samples from colicky infants given L. reuteri DSM 17938 or placebo. Twenty-nine colicky infants (age 10-60 days) were enrolled and randomly assigned to receive either Lactobacillus reuteri (10(8) cfu) or a placebo once daily for 21 days. Responders were defined as subjects with a decrease of 50% in daily crying time at day 21 compared with the starting point. The microbiota of faecal samples from day 1 and 21 were analyzed using 454 pyrosequencing. The primers: Bakt_341F and Bakt_805R, complemented with 454 adapters and sample specific barcodes were used for PCR amplification of the 16 S rRNA genes. The structure of the data was explored by using permutational multivariate analysis of variance and effects of different variables were visualized with ordination analysis. The infants' faecal microbiota were composed of Proteobacteria, Firmicutes, Actinobacteria and Bacteroidetes as the four main phyla. The composition of the microbiota in infants with colic had very high inter-individual variability with Firmicutes/Bacteroidetes ratios varying from 4000 to 0.025. On an individual basis, the microbiota was, however, relatively stable over time. Treatment with L. reuteri DSM 17938 did not change the global composition of the microbiota, but when comparing responders with non-responders the group responders had an increased relative abundance of the phyla Bacteroidetes and genus Bacteroides at day 21 compared with day 0. Furthermore, the phyla composition of the infants at day 21 could be divided into three enterotype groups, dominated by Firmicutes, Bacteroidetes, and Actinobacteria, respectively. L. reuteri DSM 17938 did not affect the global composition of the microbiota. However, the increase of Bacteroidetes in the responder infants indicated that a decrease in colicky symptoms was linked to changes of the microbiota. ClinicalTrials.gov NCT00893711.

Bacterial colonization of a fumigated alkaline saline soil.

PubMed

Bello-López, Juan M; Domínguez-Mendoza, Cristina A; de León-Lorenzana, Arit S; Delgado-Balbuena, Laura; Navarro-Noya, Yendi E; Gómez-Acata, Selene; Rodríguez-Valentín, Analine; Ruíz-Valdiviezo, Victor M; Luna-Guido, Marco; Verhulst, Nele; Govaerts, Bram; Dendooven, Luc

2014-07-01

After chloroform fumigating an arable soil, the relative abundance of phylotypes belonging to only two phyla (Actinobacteria and Firmicutes) and two orders [Actinomycetales and Bacillales (mostly Bacillus)] increased in a subsequent aerobic incubation, while it decreased for a wide range of bacterial groups. It remained to be seen if similar bacterial groups were affected when an extreme alkaline saline soil was fumigated. Soil with electrolytic conductivity between 139 and 157 dS m(-1), and pH 10.0 and 10.3 was fumigated and the bacterial community structure determined after 0, 1, 5 and 10 days by analysis of the 16S rRNA gene, while an unfumigated soil served as control. The relative abundance of the Firmicutes increased in the fumigated soil (52.8%) compared to the unfumigated soil (34.2%), while that of the Bacteroidetes decreased from 16.2% in the unfumigated soil to 8.8% in the fumigated soil. Fumigation increased the relative abundance of the genus Bacillus from 14.7% in the unfumigated soil to 25.7%. It was found that phylotypes belonging to the Firmicutes, mostly of the genus Bacillus, were dominant in colonizing the fumigated alkaline saline as found in the arable soil, while the relative abundance of a wide range of bacterial groups decreased.

Analysis of the bacterial community in aged and aging pit mud of Chinese Luzhou-flavour liquor by combined PCR-DGGE and quantitative PCR assay.

PubMed

Liang, Huipeng; Li, Wenfang; Luo, Qingchun; Liu, Chaolan; Wu, Zhengyun; Zhang, Wenxue

2015-10-01

The community structure of bacteria in aged and aging pit mud, which was judged according to their sensory and physicochemical characteristics, was analysed using polymerase chain reaction denaturing gradient gel electrophoresis (PCR-DGGE) and quantitative real-time PCR (qPCR). The phyla Firmicutes, Actinobacteria, Proteobacteria, Synergistetes and Unclassified Bacteria were detected and the fermentative Firmicutes was predominant in both types of pit mud in the PCR-DGGE analysis. Among Firmicutes, Clostridiales was dominant in aged pit mud while Bacillales and Lactobacillales were dominant in aging pit mud. The diversity of bacterial communities in aged pit mud was higher than that in aging pit mud. In the qPCR analysis the abundance of Clostridium IV in aged pit mud was higher than that in aging pit mud and there were significant differences in the quantity of Clostridium IV between aged and aging pit mud of the same cellar (P < 0.05). There were some significant differences in the microbial community structure between aged and aging pit mud. The differences in the quantity of Clostridium IV might be involved in the distinction that the aged pit mud has a strong aroma while the aging pit mud does not. © 2014 Society of Chemical Industry.

Selection of an actinobacteria mixed culture for chlordane remediation. Pesticide effects on microbial morphology and bioemulsifier production.

PubMed

Fuentes, María S; Colin, Verónica L; Amoroso, María J; Benimeli, Claudia S

2016-02-01

Chlordane bioremediation using actinobacteria mixed culture is an attractive clean-up technique. Their ability to produce bioemulsifiers could increase the bioavailability of this pesticide. In order to select a defined actinobacteria mixed culture for chlordane remediation, compatibility assays were performed among six Streptomyces strains. The strains did not show growth inhibition, and they were assayed for chlordane removal, either as pure or as mixed cultures. In pure cultures, all of the strains showed specific dechlorination activity (1.42-24.20 EU mg(-1)) and chlordane removal abilities (91.3-95.5%). The specific dechlorination activity was mainly improved with cultures of three or four microorganisms. The mixed culture consisting of Streptomyces sp. A2-A5-A13 was selected. Their ability to produce bioemulsifiers in the presence of glucose or chlordane was tested, but no significant differences were observed (p > 0.05). However, the stability of the emulsions formed was linked to the carbon source used. Only in chlordane presence the emulsions retained 100% of their initial height. Finally, the selected consortium showed a high degree of sporulation in the pesticide presence. This is the first study on the effects that chlordane exerts on microbe morphology and emulsifier production for a defined mixed culture of Streptomyces with ability to remediate the pesticide. © 2015 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

Exploration of Microbial Diversity and Community Structure of Lonar Lake: The Only Hypersaline Meteorite Crater Lake within Basalt Rock

PubMed Central

Paul, Dhiraj; Kumbhare, Shreyas V.; Mhatre, Snehit S.; Chowdhury, Somak P.; Shetty, Sudarshan A.; Marathe, Nachiket P.; Bhute, Shrikant; Shouche, Yogesh S.

2016-01-01

Lonar Lake is a hypersaline and hyperalkaline soda lake and the only meteorite impact crater in the world situated in basalt rocks. Although culture-dependent studies have been reported, a comprehensive understanding of microbial community composition and structure in Lonar Lake remains elusive. In the present study, microbial community structure associated with Lonar Lake sediment and water samples was investigated using high-throughput sequencing. Microbial diversity analysis revealed the existence of diverse, yet largely consistent communities. Proteobacteria (30%), Actinobacteria (24%), Firmicutes (11%), and Cyanobacteria (5%) predominated in the sequencing survey, whereas Bacteroidetes (1.12%), BD1-5 (0.5%), Nitrospirae (0.41%), and Verrucomicrobia (0.28%) were detected in relatively minor abundances in the Lonar Lake ecosystem. Within the Proteobacteria phylum, the Gammaproteobacteria represented the most abundantly detected class (21–47%) within sediment samples, but only a minor population in the water samples. Proteobacteria and Firmicutes were found at significantly higher abundance (p ≥ 0.05) in sediment samples, whereas members of Actinobacteria, Candidate division TM7 and Cyanobacteria (p ≥ 0.05) were significantly abundant in water samples. Compared to the microbial communities of other hypersaline soda lakes, those of Lonar Lake formed a distinct cluster, suggesting a different microbial community composition and structure. Here we report for the first time, the difference in composition of indigenous microbial communities between the sediment and water samples of Lonar Lake. An improved census of microbial community structure in this Lake ecosystem provides a foundation for exploring microbial biogeochemical cycling and microbial function in hypersaline lake environments. PMID:26834712

[The composition of the gastrointestinal bacterial flora of mouse embryos and the placenta tissue bacterial flora].

PubMed

Lei, D; Lin, Y; Jiang, X; Lan, L; Zhang, W; Wang, B X

2017-03-02

Objective: To explore the composition of the gastrointestinal bacterial flora of mouse embryos and the placenta tissue bacterial flora. Method: Twenty-four specimens were collected from pregnant Kunming mouse including 8 mice of early embryonic (12-13 days) gastrointestinal tissues, 8 cases of late embryonic (19-20 days)gastrointestinal tissues, 8 of late pregnancy placental tissues.The 24 samples were extracted by DNeasy Blood & Tissue kit for high-throughput DNA sequencing. Result: The level of Proteobacteria, Bacteroidetes, Actino-bacteria and Firmicutes were predominantin all specimens.The relative content of predominant bacterial phyla in each group: Proteobacteria (95.00%, 88.14%, 87.26%), Bacteroidetes(1.71%, 2.15%, 2.63%), Actino-Bacteria(1.16%, 4.10%, 3.38%), Firmicutes(0.75%, 2.62%, 2.01%). At the level of family, there were nine predominant bacterial families in which Enterobacteriaeae , Shewanel laceae and Moraxellaceae were dominant.The relative content of dominant bacterial family in eachgroup: Enterobacteriaeae (46.99%, 44.34%, 41.08%), Shewanellaceae (21.99%, 21.10%, 19.05%), Moraxellaceae (9.18%, 7.09%, 5.64%). From the species of flora, the flora from fetal gastrointestinal in early pregnancy and late pregnancy (65.44% and 62.73%) were the same as that from placenta tissue in the late pregnancy.From the abundance of bacteria, at the level of family, the same content of bacteria in three groups accounted for 78.16%, 72.53% and 65.78% respectively. Conclusion: It was proved that the gastrointestinal bacterial flora of mouse embryos and the placenta tissue bacterial flora were colonized. At the same time the bacteria are classified.

Adapt or Die on the Highway To Hell: Metagenomic Insights into Altered Genomes of Firmicutes from the Deep Biosphere

NASA Astrophysics Data System (ADS)

Briggs, B. R.; Colwell, F. S.

2014-12-01

The ability of a microbe to persist in low-nutrient environments requires adaptive mechanisms to survive. These microorganisms must reduce metabolic energy and increase catabolic efficiency. For example, Escherichia coli surviving in low-nutrient extended stationary phase have mutations that confer a growth advantage in stationary phase (GASP) phenotype, thus allowing for persistence for years in low-nutrient environments. Based on the fact that subseafloor environments are characterized by energy flux decrease with time of burial we hypothesize that cells from older (deeper) sediment layers will have more altered genomes compared to sequenced surface relatives and that these differences reflect adaptations to a low-energy flux environment. To test this hypothesis, sediment samples were collected from the Andaman Sea from the depths of 21, 40 and 554 meters below seafloor, with the ages of 0.34, 0.66, and 8.76 million years, respectively. A single operational taxonomic unit within Firmicutes, based on full-length 16S rDNA, dominated these low diversity samples. This unique feature allowed for metagenomic sequencing using the Illumina HiSeq to identify nucleotide variations (NV) between the subsurface Firmicutes and the closest sequenced representative, Bacillus subtilis BEST7613. NVs were present at all depths in genes that code for proteins used in energy-dependent proteolysis, cell division, sporulation, and (similar to the GASP mutants) biosynthetic pathways for amino acids, nucleotides, and fatty acids. Conserved genes such as 16S rDNA did not contain NVs. More NVs were found in genes from deeper depths. These NV may be beneficial or harmful allowing them to survive for millions of years in the deep biosphere or may be latent deleterious gene alterations that are masked by the minimal-growth status of these deep microbes. Either way these results show that microbes present in the deep biosphere experience environmental forcing that alters the genome.

Bacterial community composition and structure in an Urban River impacted by different pollutant sources.

PubMed

Ibekwe, A Mark; Ma, Jincai; Murinda, Shelton E

2016-10-01

Microbial communities in terrestrial fresh water are diverse and dynamic in composition due to different environmental factors. The goal of this study was to undertake a comprehensive analysis of bacterial composition along different rivers and creeks and correlate these to land-use practices and pollutant sources. Here we used 454 pyrosequencing to determine the total bacterial community composition, and bacterial communities that are potentially of fecal origin, and of relevance to water quality assessment. The results were analyzed using UniFrac coupled with principal coordinate analysis (PCoA) to compare diversity, abundance, and community composition. Detrended correspondence analysis (DCA) and canonical correspondence analysis (CCA) were used to correlate bacterial composition in streams and creeks to different environmental parameters impacting bacterial communities in the sediment and surface water within the watershed. Bacteria were dominated by the phyla Proteobacteria, Bacteroidetes, Acidobacteria, and Actinobacteria, with Bacteroidetes significantly (P<0.001) higher in all water samples than sediment, where as Acidobacteria and Actinobacteria where significantly higher (P<0.05) in all the sediment samples than surface water. Overall results, using the β diversity measures, coupled with PCoA and DCA showed that bacterial composition in sediment and surface water was significantly different (P<0.001). Also, there were differences in bacterial community composition between agricultural runoff and urban runoff based on parsimony tests using 454 pyrosequencing data. Fecal indicator bacteria in surface water along different creeks and channels were significantly correlated with pH (P<0.01), NO2 (P<0.03), and NH4N (P<0.005); and in the sediment with NO3 (P<0.015). Our results suggest that microbial community compositions were influenced by several environmental factors, and pH, NO2, and NH4 were the major environmental factors driving FIB in surface water

16S Based Microbiome Analysis from Healthy Subjects’ Skin Swabs Stored for Different Storage Periods Reveal Phylum to Genus Level Changes

PubMed Central

Klymiuk, Ingeborg; Bambach, Isabella; Patra, Vijaykumar; Trajanoski, Slave; Wolf, Peter

2016-01-01

in the ratios of the main phyla Actinobacteria, Firmicutes, and Bacteroidetes: Actinobacteria vs. Bacteroidetes at d0 vs. d90 (p-value = 0.0234), at d0 vs. d365 (p-value = 0.0234) and d90 vs. d365 (p-value = 0.0234) in forearm samples and at d90 vs. d365 in V of the chest (p-value = 0.0234) and back samples (p-value = 0.0234). The ratios of Firmicutes vs. Bacteroidetes showed no significant changes in any of the body locations as well as the ratios of Actinobacteria vs. Firmicutes at any time point. Studies with larger sample sizes are required to verify our results and determine long term storage effects with regard to specific biological questions. PMID:28066342

Bacterial populations and environmental factors controlling cellulose degradation in an acidic Sphagnum peat.

PubMed

Pankratov, Timofey A; Ivanova, Anastasia O; Dedysh, Svetlana N; Liesack, Werner

2011-07-01

Northern peatlands represent a major global carbon store harbouring approximately one-third of the global reserves of soil organic carbon. A large proportion of these peatlands consists of acidic Sphagnum-dominated ombrotrophic bogs, which are characterized by extremely low rates of plant debris decomposition. The degradation of cellulose, the major component of Sphagnum-derived litter, was monitored in long-term incubation experiments with acidic (pH 4.0) peat extracts. This process was almost undetectable at 10°C and occurred at low rates at 20°C, while it was significantly accelerated at both temperature regimes by the addition of available nitrogen. Cellulose breakdown was only partially inhibited in the presence of cycloheximide, suggesting that bacteria participated in this process. We aimed to identify these bacteria by a combination of molecular and cultivation approaches and to determine the factors that limit their activity in situ. The indigenous bacterial community in peat was dominated by Alphaproteobacteria and Acidobacteria. The addition of cellulose induced a clear shift in the community structure towards an increase in the relative abundance of the Bacteroidetes. Increasing temperature and nitrogen availability resulted in a selective development of bacteria phylogenetically related to Cytophaga hutchinsonii (94-95% 16S rRNA gene sequence similarity), which densely colonized microfibrils of cellulose. Among isolates obtained from this community only some subdivision 1 Acidobacteria were capable of degrading cellulose, albeit at a very slow rate. These Acidobacteria represent indigenous cellulolytic members of the microbial community in acidic peat and are easily out-competed by Cytophaga-like bacteria under conditions of increased nitrogen availability. Members of the phylum Firmicutes, known to be key players in cellulose degradation in neutral habitats, were not detected in the cellulolytic community enriched at low pH. © 2011 Society for

Regulation of specialised metabolites in Actinobacteria - expanding the paradigms.

PubMed

Hoskisson, Paul A; Fernández-Martínez, Lorena T

2018-06-01

The increase in availability of actinobacterial whole genome sequences has revealed huge numbers of specialised metabolite biosynthetic gene clusters, encoding a range of bioactive molecules such as antibiotics, antifungals, immunosuppressives and anticancer agents. Yet the majority of these clusters are not expressed under standard laboratory conditions in rich media. Emerging data from studies of specialised metabolite biosynthesis suggest that the diversity of regulatory mechanisms is greater than previously thought and these act at multiple levels, through a range of signals such as nutrient limitation, intercellular signalling and competition with other organisms. Understanding the regulation and environmental cues that lead to the production of these compounds allows us to identify the role that these compounds play in their natural habitat as well as provide tools to exploit this untapped source of specialised metabolites for therapeutic uses. Here, we provide an overview of novel regulatory mechanisms that act in physiological, global and cluster-specific regulatory manners on biosynthetic pathways in Actinobacteria and consider these alongside their ecological and evolutionary implications. © 2018 The Authors. Environmental Microbiology published by Society for Applied Microbiology and JohnWiley & Sons Ltd.

Regulation of specialised metabolites in Actinobacteria – expanding the paradigms

PubMed Central

Hoskisson, Paul A.

2018-01-01

Summary The increase in availability of actinobacterial whole genome sequences has revealed huge numbers of specialised metabolite biosynthetic gene clusters, encoding a range of bioactive molecules such as antibiotics, antifungals, immunosuppressives and anticancer agents. Yet the majority of these clusters are not expressed under standard laboratory conditions in rich media. Emerging data from studies of specialised metabolite biosynthesis suggest that the diversity of regulatory mechanisms is greater than previously thought and these act at multiple levels, through a range of signals such as nutrient limitation, intercellular signalling and competition with other organisms. Understanding the regulation and environmental cues that lead to the production of these compounds allows us to identify the role that these compounds play in their natural habitat as well as provide tools to exploit this untapped source of specialised metabolites for therapeutic uses. Here, we provide an overview of novel regulatory mechanisms that act in physiological, global and cluster‐specific regulatory manners on biosynthetic pathways in Actinobacteria and consider these alongside their ecological and evolutionary implications. PMID:29457705

Properties of Soil Pore Space Regulate Pathways of Plant Residue Decomposition and Community Structure of Associated Bacteria

PubMed Central

Negassa, Wakene C.; Guber, Andrey K.; Kravchenko, Alexandra N.; Marsh, Terence L.; Hildebrandt, Britton; Rivers, Mark L.

2015-01-01

Physical protection of soil carbon (C) is one of the important components of C storage. However, its exact mechanisms are still not sufficiently lucid. The goal of this study was to explore the influence of soil structure, that is, soil pore spatial arrangements, with and without presence of plant residue on (i) decomposition of added plant residue, (ii) CO2 emission from soil, and (iii) structure of soil bacterial communities. The study consisted of several soil incubation experiments with samples of contrasting pore characteristics with/without plant residue, accompanied by X-ray micro-tomographic analyses of soil pores and by microbial community analysis of amplified 16S–18S rRNA genes via pyrosequencing. We observed that in the samples with substantial presence of air-filled well-connected large (>30 µm) pores, 75–80% of the added plant residue was decomposed, cumulative CO2 emission constituted 1,200 µm C g-1 soil, and movement of C from decomposing plant residue into adjacent soil was insignificant. In the samples with greater abundance of water-filled small pores, 60% of the added plant residue was decomposed, cumulative CO2 emission constituted 2,000 µm C g-1 soil, and the movement of residue C into adjacent soil was substantial. In the absence of plant residue the influence of pore characteristics on CO2 emission, that is on decomposition of the native soil organic C, was negligible. The microbial communities on the plant residue in the samples with large pores had more microbial groups known to be cellulose decomposers, that is, Bacteroidetes, Proteobacteria, Actinobacteria, and Firmicutes, while a number of oligotrophic Acidobacteria groups were more abundant on the plant residue from the samples with small pores. This study provides the first experimental evidence that characteristics of soil pores and their air/water flow status determine the phylogenetic composition of the local microbial community and directions and magnitudes of soil C

Properties of soil pore space regulate pathways of plant residue decomposition and community structure of associated bacteria

DOE PAGES

Negassa, Wakene C.; Guber, Andrey K.; Kravchenko, Alexandra N.; ...

2015-07-01

Physical protection of soil carbon (C) is one of the important components of C storage. However, its exact mechanisms are still not sufficiently lucid. The goal of this study was to explore the influence of soil structure, that is, soil pore spatial arrangements, with and without presence of plant residue on (i) decomposition of added plant residue, (ii) CO₂ emission from soil, and (iii) structure of soil bacterial communities. The study consisted of several soil incubation experiments with samples of contrasting pore characteristics with/without plant residue, accompanied by X-ray micro-tomographic analyses of soil pores and by microbial community analysis ofmore » amplified 16S–18S rRNA genes via pyrosequencing. We observed that in the samples with substantial presence of air-filled well-connected large (>30 µm) pores, 75–80% of the added plant residue was decomposed, cumulative CO₂ emission constituted 1,200 µm C g⁻¹ soil, and movement of C from decomposing plant residue into adjacent soil was insignificant. In the samples with greater abundance of water-filled small pores, 60% of the added plant residue was decomposed, cumulative CO₂ emission constituted 2,000 µm C g⁻¹ soil, and the movement of residue C into adjacent soil was substantial. In the absence of plant residue the influence of pore characteristics on CO₂ emission, that is on decomposition of the native soil organic C, was negligible. The microbial communities on the plant residue in the samples with large pores had more microbial groups known to be cellulose decomposers, that is, Bacteroidetes, Proteobacteria, Actinobacteria, and Firmicutes, while a number of oligotrophic Acidobacteria groups were more abundant on the plant residue from the samples with small pores. This study provides the first experimental evidence that characteristics of soil pores and their air/water flow status determine the phylogenetic composition of the local microbial community and directions and

Culture dependent and independent analysis of bacterial communities associated with commercial salad leaf vegetables.

PubMed

Jackson, Colin R; Randolph, Kevin C; Osborn, Shelly L; Tyler, Heather L

2013-12-01

Plants harbor a diverse bacterial community, both as epiphytes on the plant surface and as endophytes within plant tissue. While some plant-associated bacteria act as plant pathogens or promote plant growth, others may be human pathogens. The aim of the current study was to determine the bacterial community composition of organic and conventionally grown leafy salad vegetables at the point of consumption using both culture-dependent and culture-independent methods. Total culturable bacteria on salad vegetables ranged from 8.0 × 10(3) to 5.5 × 10(8) CFU g(-1). The number of culturable endophytic bacteria from surface sterilized plants was significantly lower, ranging from 2.2 × 10(3) to 5.8 × 10(5) CFU g(-1). Cultured isolates belonged to six major bacterial phyla, and included representatives of Pseudomonas, Pantoea, Chryseobacterium, and Flavobacterium. Eleven different phyla and subphyla were identified by culture-independent pyrosequencing, with Gammaproteobacteria, Betaproteobacteria, and Bacteroidetes being the most dominant lineages. Other bacterial lineages identified (e.g. Firmicutes, Alphaproteobacteria, Acidobacteria, and Actinobacteria) typically represented less than 1% of sequences obtained. At the genus level, sequences classified as Pseudomonas were identified in all samples and this was often the most prevalent genus. Ralstonia sequences made up a greater portion of the community in surface sterilized than non-surface sterilized samples, indicating that it was largely endophytic, while Acinetobacter sequences appeared to be primarily associated with the leaf surface. Analysis of molecular variance indicated there were no significant differences in bacterial community composition between organic versus conventionally grown, or surface-sterilized versus non-sterilized leaf vegetables. While culture-independent pyrosequencing identified significantly more bacterial taxa, the dominant taxa from pyrosequence data were also detected by traditional

Culture dependent and independent analysis of bacterial communities associated with commercial salad leaf vegetables

PubMed Central

2013-01-01

Background Plants harbor a diverse bacterial community, both as epiphytes on the plant surface and as endophytes within plant tissue. While some plant-associated bacteria act as plant pathogens or promote plant growth, others may be human pathogens. The aim of the current study was to determine the bacterial community composition of organic and conventionally grown leafy salad vegetables at the point of consumption using both culture-dependent and culture-independent methods. Results Total culturable bacteria on salad vegetables ranged from 8.0 × 103 to 5.5 × 108 CFU g-1. The number of culturable endophytic bacteria from surface sterilized plants was significantly lower, ranging from 2.2 × 103 to 5.8 × 105 CFU g-1. Cultured isolates belonged to six major bacterial phyla, and included representatives of Pseudomonas, Pantoea, Chryseobacterium, and Flavobacterium. Eleven different phyla and subphyla were identified by culture-independent pyrosequencing, with Gammaproteobacteria, Betaproteobacteria, and Bacteroidetes being the most dominant lineages. Other bacterial lineages identified (e.g. Firmicutes, Alphaproteobacteria, Acidobacteria, and Actinobacteria) typically represented less than 1% of sequences obtained. At the genus level, sequences classified as Pseudomonas were identified in all samples and this was often the most prevalent genus. Ralstonia sequences made up a greater portion of the community in surface sterilized than non-surface sterilized samples, indicating that it was largely endophytic, while Acinetobacter sequences appeared to be primarily associated with the leaf surface. Analysis of molecular variance indicated there were no significant differences in bacterial community composition between organic versus conventionally grown, or surface-sterilized versus non-sterilized leaf vegetables. While culture-independent pyrosequencing identified significantly more bacterial taxa, the dominant taxa from pyrosequence data were also detected by

Properties of soil pore space regulate pathways of plant residue decomposition and community structure of associated bacteria

DOE Office of Scientific and Technical Information (OSTI.GOV)

Negassa, Wakene C.; Guber, Andrey K.; Kravchenko, Alexandra N.

Physical protection of soil carbon (C) is one of the important components of C storage. However, its exact mechanisms are still not sufficiently lucid. The goal of this study was to explore the influence of soil structure, that is, soil pore spatial arrangements, with and without presence of plant residue on (i) decomposition of added plant residue, (ii) CO₂ emission from soil, and (iii) structure of soil bacterial communities. The study consisted of several soil incubation experiments with samples of contrasting pore characteristics with/without plant residue, accompanied by X-ray micro-tomographic analyses of soil pores and by microbial community analysis ofmore » amplified 16S–18S rRNA genes via pyrosequencing. We observed that in the samples with substantial presence of air-filled well-connected large (>30 µm) pores, 75–80% of the added plant residue was decomposed, cumulative CO₂ emission constituted 1,200 µm C g⁻¹ soil, and movement of C from decomposing plant residue into adjacent soil was insignificant. In the samples with greater abundance of water-filled small pores, 60% of the added plant residue was decomposed, cumulative CO₂ emission constituted 2,000 µm C g⁻¹ soil, and the movement of residue C into adjacent soil was substantial. In the absence of plant residue the influence of pore characteristics on CO₂ emission, that is on decomposition of the native soil organic C, was negligible. The microbial communities on the plant residue in the samples with large pores had more microbial groups known to be cellulose decomposers, that is, Bacteroidetes, Proteobacteria, Actinobacteria, and Firmicutes, while a number of oligotrophic Acidobacteria groups were more abundant on the plant residue from the samples with small pores. This study provides the first experimental evidence that characteristics of soil pores and their air/water flow status determine the phylogenetic composition of the local microbial community and directions and

Analysis of potential risks from the bacterial communities associated with air-contact surfaces from tilapia (Oreochromis niloticus) fish farming.

PubMed

Grande Burgos, Maria Jose; Romero, Jose Luis; Pérez Pulido, Rubén; Cobo Molinos, Antonio; Gálvez, Antonio; Lucas, Rosario

2018-01-01

Tilapia farming is a promising growing sector in aquaculture. Yet, there are limited studies on microbiological risks associated to tilapia farms. The aim of the present study was to analyse the bacterial communities from solid surfaces in contact with air in a tilapia farm in order to evaluate the presence of bacteria potentially toxinogenic or pathogenic to humans or animals. Samples from a local tilapia farm (tank wall, aerator, water outlets, sink and floor) were analyzed by high throughput sequencing technology. Sequences were assigned to operational taxonomic units (OTUs). Proteobacteria was the main phylum represented in most samples (except for one). Cyanobacteria were a relevant phylum in the inner wall from the fattening tank and the wet floor by the pre-fattening tank. Bacteroidetes were the second phylum in relative abundance for samples from the larval rearing tank and the pre-fattening tank and one sample from the fattening tank. Fusobacteria showed highest relative abundances in samples from the larval rearing tank and pre-fattening tank. Other phyla (Verrucomicrobia, Actinobacteria, Firmicutes, Planktomycetes, Acidobacteria, Chloroflexi, Chlorobi, Gemmatiomonadetes or Fibrobacters) had lower relative abundances. A large fraction of the reads (ranging from 43.67% to 72.25%) were assigned to uncultured bacteria. Genus Acinetobacter (mainly A. calcoaceticus/baumanni) was the predominant OTU in the aerator of the fattening tank and also in the nearby sink on the floor. The genera Cetobacterium and Bacteroides showed highest relative abundances in the samples from the larval rearing tank and the pre-fattening tank. Genera including fish pathogens (Fusobacterium, Aeromonas) were only detected at low relative abundances. Potential human pathogens other than Acinetobacter were either not detected or had very low relative abundances (< 0.01%). The results of the study suggest that the main risk factors to be monitored in tilapia farm are putative human

Properties of soil pore space regulate pathways of plant residue decomposition and community structure of associated bacteria.

PubMed

Negassa, Wakene C; Guber, Andrey K; Kravchenko, Alexandra N; Marsh, Terence L; Hildebrandt, Britton; Rivers, Mark L

2015-01-01

Physical protection of soil carbon (C) is one of the important components of C storage. However, its exact mechanisms are still not sufficiently lucid. The goal of this study was to explore the influence of soil structure, that is, soil pore spatial arrangements, with and without presence of plant residue on (i) decomposition of added plant residue, (ii) CO2 emission from soil, and (iii) structure of soil bacterial communities. The study consisted of several soil incubation experiments with samples of contrasting pore characteristics with/without plant residue, accompanied by X-ray micro-tomographic analyses of soil pores and by microbial community analysis of amplified 16S-18S rRNA genes via pyrosequencing. We observed that in the samples with substantial presence of air-filled well-connected large (>30 µm) pores, 75-80% of the added plant residue was decomposed, cumulative CO2 emission constituted 1,200 µm C g(-1) soil, and movement of C from decomposing plant residue into adjacent soil was insignificant. In the samples with greater abundance of water-filled small pores, 60% of the added plant residue was decomposed, cumulative CO2 emission constituted 2,000 µm C g(-1) soil, and the movement of residue C into adjacent soil was substantial. In the absence of plant residue the influence of pore characteristics on CO2 emission, that is on decomposition of the native soil organic C, was negligible. The microbial communities on the plant residue in the samples with large pores had more microbial groups known to be cellulose decomposers, that is, Bacteroidetes, Proteobacteria, Actinobacteria, and Firmicutes, while a number of oligotrophic Acidobacteria groups were more abundant on the plant residue from the samples with small pores. This study provides the first experimental evidence that characteristics of soil pores and their air/water flow status determine the phylogenetic composition of the local microbial community and directions and magnitudes of soil C

Contrasting bacterial communities in two indigenous Chionochloa (Poaceae) grassland soils in New Zealand

PubMed Central

Griffith, Jocelyn C.; Lee, William G.; Orlovich, David A.

2017-01-01

The cultivation of grasslands can modify both bacterial community structure and impact on nutrient cycling as well as the productivity and diversity of plant communities. In this study, two pristine New Zealand grassland sites dominated by indigenous tall tussocks (Chionochloa pallens or C. teretifolia) were examined to investigate the extent and predictability of variation of the bacterial community. The contribution of free-living bacteria to biological nitrogen fixation is predicted to be ecologically significant in these soils; therefore, the diazotrophic community was also examined. The C. teretifolia site had N-poor and poorly-drained peaty soils, and the C. pallens had N-rich and well-drained fertile soils. These soils also differ in the proportion of organic carbon (C), Olsen phosphorus (P) and soil pH. The nutrient-rich soils showed increased relative abundances of some copiotrophic bacterial taxa (including members of the Proteobacteria, Bacteroidetes and Firmicutes phyla). Other copiotrophs, Actinobacteria and the oliogotrophic Acidobacteria showed increased relative abundance in nutrient-poor soils. Greater diversity based on 16S rRNA gene sequences and the Tax4Fun prediction of enhanced spore formation associated with nutrient-rich soils could indicate increased resilience of the bacterial community. The two sites had distinct diazotrophic communities with higher diversity in C. teretifolia soils that had less available nitrate and ammonium, potentially indicating increased resilience of the diazotroph community at this site. The C. teretifolia soils had more 16S rRNA gene and nifH copies per g soil than the nutrient rich site. However, the proportion of the bacterial community that was diazotrophic was similar in the two soils. We suggest that edaphic and vegetation factors are contributing to major differences in the composition and diversity of total bacterial and diazotrophic communities at these sites. We predict the differences in the communities

Long-term field application of sewage sludge increases the abundance of antibiotic resistance genes in soil.

PubMed

Chen, Qinglin; An, Xinli; Li, Hu; Su, Jianqiang; Ma, Yibing; Zhu, Yong-Guan

2016-01-01

Sewage sludge and manure are common soil amendments in crop production; however, their impact on the abundance and diversity of the antibiotic resistome in soil remains elusive. In this study, by using high-throughput sequencing and high-throughput quantitative PCR, the patterns of bacterial community and antibiotic resistance genes (ARGs) in a long-term field experiment were investigated to gain insights into these impacts. A total of 130 unique ARGs and 5 mobile genetic elements (MGEs) were detected and the long-term application of sewage sludge and chicken manure significantly increased the abundance and diversity of ARGs in the soil. Genes conferring resistance to beta-lactams, tetracyclines, and multiple drugs were dominant in the samples. Sewage sludge or chicken manure applications caused significant enrichment of 108 unique ARGs and MGEs with a maximum enrichment of up to 3845 folds for mexF. The enrichment of MGEs suggested that the application of sewage sludge or manure may accelerate the dissemination of ARGs in soil through horizontal gene transfer (HGT). Based on the co-occurrence pattern of ARGs subtypes revealed by network analysis, aacC, oprD and mphA-02, were proposed to be potential indicators for quantitative estimation of the co-occurring ARGs subtypes abundance by power functions. The application of sewage sludge and manure resulted in significant increase of bacterial diversity in soil, Proteobacteria, Acidobacteria, Actinobacteria and Chloroflexi were the dominant phyla (>10% in each sample). Five bacterial phyla (Chloroflexi, Planctomycetes, Firmicutes, Gemmatimonadetes and Bacteroidetes) were found to be significantly correlated with the ARGs in soil. Mantel test and variation partitioning analysis (VPA) suggested that bacterial community shifts, rather than MGEs, is the major driver shaping the antibiotic resistome. Additionally, the co-occurrence pattern between ARGs and microbial taxa revealed by network analysis indicated that four

Cultured bacterial diversity and human impact on alpine glacier cryoconite.

PubMed

Lee, Yung Mi; Kim, So-Yeon; Jung, Jia; Kim, Eun Hye; Cho, Kyeung Hee; Schinner, Franz; Margesin, Rosa; Hong, Soon Gyu; Lee, Hong Kum

2011-06-01

The anthropogenic effect on the microbial communities in alpine glacier cryoconites was investigated by cultivation and physiological characterization of bacteria from six cryoconite samples taken at sites with different amounts of human impact. Two hundred and forty seven bacterial isolates were included in Actinobacteria (9%, particularly Arthrobacter), Bacteroidetes (14%, particularly Olleya), Firmicutes (0.8%), Alphaproteobacteria (2%), Betaproteobacteria (16%, particularly Janthinobacterium), and Gammaproteobacteria (59%, particularly Pseudomonas). Among them, isolates of Arthrobacter were detected only in samples from sites with no human impact, while isolates affiliated with Enterobacteriaceae were detected only in samples from sites with strong human impact. Bacterial isolates included in Actinobacteria and Bacteroidetes were frequently isolated from pristine sites and showed low maximum growth temperature and enzyme secretion. Bacterial isolates included in Gammaproteobacteria were more frequently isolated from sites with stronger human impact and showed high maximum growth temperature and enzyme secretion. Ecotypic differences were not evident among isolates of Janthinobacterium lividum, Pseudomonas fluorescens, and Pseudomonas veronii, which were frequently isolated from sites with different degrees of anthropogenic effect.

Comparison of the Oral Microbiomes of Canines and Their Owners Using Next-Generation Sequencing.

PubMed

Oh, Changin; Lee, Kunkyu; Cheong, Yeotaek; Lee, Sang-Won; Park, Seung-Yong; Song, Chang-Seon; Choi, In-Soo; Lee, Joong-Bok

2015-01-01

The oral microbiome, which is closely associated with many diseases, and the resident pathogenic oral bacteria, which can be transferred by close physical contact, are important public health considerations. Although the dog is the most common companion animal, the composition of the canine oral microbiome, which may include human pathogenic bacteria, and its relationship with that of their owners are unclear. In this study, 16S rDNA pyrosequencing was used to compare the oral microbiomes of 10 dogs and their owners and to identify zoonotic pathogens. Pyrosequencing revealed 246 operational taxonomic units in the 10 samples, representing 57 genera from eight bacterial phyla. Firmicutes (57.6%), Proteobacteria (21.6%), Bacteroidetes (9.8%), Actinobacteria (7.1%), and Fusobacteria (3.9%) were the predominant phyla in the human oral samples, whereas Proteobacteria (25.7%), Actinobacteria (21%), Bacteroidetes (19.7%), Firmicutes (19.3%), and Fusobacteria (12.3%) were predominant in the canine oral samples. The predominant genera in the human samples were Streptococcus (43.9%), Neisseria (10.3%), Haemophilus (9.6%), Prevotella (8.4%), and Veillonella (8.1%), whereas the predominant genera in the canine samples were Actinomyces (17.2%), Unknown (16.8), Porphyromonas (14.8), Fusobacterium (11.8), and Neisseria (7.2%). The oral microbiomes of dogs and their owners were appreciably different, and similarity in the microbiomes of canines and their owners was not correlated with residing in the same household. Oral-to-oral transfer of Neisseria shayeganii, Porphyromonas canigingivalis, Tannerella forsythia, and Streptococcus minor from dogs to humans was suspected. The finding of potentially zoonotic and periodontopathic bacteria in the canine oral microbiome may be a public health concern.

High-throughput sequencing reveals the core gut microbiome of Bar-headed goose (Anser indicus) in different wintering areas in Tibet.

PubMed

Wang, Wen; Cao, Jian; Yang, Fang; Wang, Xuelian; Zheng, Sisi; Sharshov, Kirill; Li, Laixing

2016-04-01

Elucidating the spatial dynamic and core gut microbiome related to wild bar-headed goose is of crucial importance for probiotics development that may meet the demands of bar-headed goose artificial breeding industries and accelerate the domestication of this species. However, the core microbial communities in the wild bar-headed geese remain totally unknown. Here, for the first time, we present a comprehensive survey of bar-headed geese gut microbial communities by Illumina high-throughput sequencing technology using nine individuals from three distinct wintering locations in Tibet. A total of 236,676 sequences were analyzed, and 607 OTUs were identified. We show that the gut microbial communities of bar-headed geese have representatives of 14 phyla and are dominated by Firmicutes, Proteobacteria, Actinobacteria, and Bacteroidetes. The additive abundance of these four most dominant phyla was above 96% across all the samples. At the genus level, the sequences represented 150 genera. A set of 19 genera were present in all samples and considered as core gut microbiome. The top seven most abundant core genera were distributed in that four dominant phyla. Among them, four genera (Lactococcus, Bacillus, Solibacillus, and Streptococcus) belonged to Firmicutes, while for other three phyla, each containing one genus, such as Proteobacteria (genus Pseudomonas), Actinobacteria (genus Arthrobacter), and Bacteroidetes (genus Bacteroides). This broad survey represents the most in-depth assessment, to date, of the gut microbes that associated with bar-headed geese. These data create a baseline for future bar-headed goose microbiology research, and make an original contribution to probiotics development for bar-headed goose artificial breeding industries. © 2015 The Authors. MicrobiologyOpen published by John Wiley & Sons Ltd.

The influence of interferon β-1b on gut microbiota composition in patients with multiple sclerosis.

PubMed

Castillo-Álvarez, F; Pérez-Matute, P; Oteo, J A; Marzo-Sola, M E

2018-06-09

The association between gut microbiota and animal models of multiple sclerosis has been well established; however, studies in humans are scarce. We performed a descriptive, cross-sectional study comparing the relative composition of gut microbiota in 30 patients with multiple sclerosis (15 treated with interferon β-1b, 15 not receiving this treatment) and 14 healthy controls using next generation sequencing. Patients with multiple sclerosis and controls showed differences in the proportion of Euryarchaeota, Firmicutes, Proteobacteria, Actinobacteria, and Lentisphaerae phyla and in 17 bacterial species. More specifically, we found significant differences in the proportion of Firmicutes, Actinobacteria, and Lentisphaerae and 6 bacteria species between controls and untreated patients; however, these differences disappeared when compared with treated patients. Untreated patients showed a significant reduction in the proportion of Prevotella copri compared to controls, while the bacteria was significantly more abundant in patients treated with interferon β-1b than in untreated patients, with levels resembling those observed in the healthy control group. We observed differences in gut microbiota composition between patients with multiple sclerosis and controls, and between patients treated and not treated with interferon β-1b. In most cases, no differences were observed between treated patients and healthy controls, particularly for P. copri levels. This suggests that the clinical improvements observed in patients with multiple sclerosis receiving interferon β-1b may result from the effect of the drug on gut microbiota. Longitudinal and functional studies are necessary to establish a causal relationship. Copyright © 2018 Sociedad Española de Neurología. Publicado por Elsevier España, S.L.U. All rights reserved.

Comparison of the Oral Microbiomes of Canines and Their Owners Using Next-Generation Sequencing

PubMed Central

Oh, Changin; Lee, Kunkyu; Cheong, Yeotaek; Lee, Sang-Won; Park, Seung-Yong; Song, Chang-Seon; Choi, In-Soo; Lee, Joong-Bok

2015-01-01

The oral microbiome, which is closely associated with many diseases, and the resident pathogenic oral bacteria, which can be transferred by close physical contact, are important public health considerations. Although the dog is the most common companion animal, the composition of the canine oral microbiome, which may include human pathogenic bacteria, and its relationship with that of their owners are unclear. In this study, 16S rDNA pyrosequencing was used to compare the oral microbiomes of 10 dogs and their owners and to identify zoonotic pathogens. Pyrosequencing revealed 246 operational taxonomic units in the 10 samples, representing 57 genera from eight bacterial phyla. Firmicutes (57.6%), Proteobacteria (21.6%), Bacteroidetes (9.8%), Actinobacteria (7.1%), and Fusobacteria (3.9%) were the predominant phyla in the human oral samples, whereas Proteobacteria (25.7%), Actinobacteria (21%), Bacteroidetes (19.7%), Firmicutes (19.3%), and Fusobacteria (12.3%) were predominant in the canine oral samples. The predominant genera in the human samples were Streptococcus (43.9%), Neisseria (10.3%), Haemophilus (9.6%), Prevotella (8.4%), and Veillonella (8.1%), whereas the predominant genera in the canine samples were Actinomyces (17.2%), Unknown (16.8), Porphyromonas (14.8), Fusobacterium (11.8), and Neisseria (7.2%). The oral microbiomes of dogs and their owners were appreciably different, and similarity in the microbiomes of canines and their owners was not correlated with residing in the same household. Oral-to-oral transfer of Neisseria shayeganii, Porphyromonas canigingivalis, Tannerella forsythia, and Streptococcus minor from dogs to humans was suspected. The finding of potentially zoonotic and periodontopathic bacteria in the canine oral microbiome may be a public health concern. PMID:26134411

Effect of Saccharomyces boulardii and Mode of Delivery on the Early Development of the Gut Microbial Community in Preterm Infants.

PubMed

Zeber-Lubecka, Natalia; Kulecka, Maria; Ambrozkiewicz, Filip; Paziewska, Agnieszka; Lechowicz, Milosz; Konopka, Ewa; Majewska, Urszula; Borszewska-Kornacka, Maria; Mikula, Michal; Cukrowska, Bozena; Ostrowski, Jerzy

2016-01-01

Recent advances in culture-independent approaches have enabled insights into the diversity, complexity, and individual variability of gut microbial communities. To examine the effect of oral administration of Saccharomyces (S.) boulardii and mode of delivery on the intestinal microbial community in preterm infants. Stool samples were collected from preterm newborns randomly divided into two groups: a probiotic-receiving group (n = 18) or a placebo group (n = 21). Samples were collected before probiotic intake (day 0), and after 2 and 6 weeks of supplementation. The composition of colonizing bacteria was assessed by 16S ribosomal RNA (rRNA) gene sequencing of fecal samples using the Ion 16S Metagenomics Kit and the Ion Torrent Personal Genome Machine platform. A total of 11932257 reads were generated, and were clustered into 459, 187, and 176 operational taxonomic units at 0 days, 2 weeks, and 6 weeks, respectively. Of the 17 identified phyla, Firmicutes Actinobacteria, Proteobacteria, and Bacteroidetes were universal. The microbial community differed at day 0 compared with at 2 weeks and 6 weeks. There was a tendency for increased bacterial diversity at 2 weeks and 6 weeks compared with day 0, and infants with a gestational age of 31 weeks or higher presented increased bacterial diversity prior to S. boulardii administration. Firmicutes and Proteobacteria remained stable during the observation period, whereas Actinobacteria and Bacteroidetes increased in abundance, the latter particularly more sharply in vaginally delivered infants. While the mode of delivery may influence the development of a microbial community, this study had not enough power to detect statistical differences between cohorts supplemented with probiotics, and in a consequence, to speculate on S. boulardii effect on gut microbiome composition in preterm newborns.

Genomic and Physiological Characterization of the Chromate-Reducing, Aquifer-Derived Firmicute Pelosinus sp. Strain HCF1

NASA Astrophysics Data System (ADS)

Beller, H. R.; Han, R.; Karaoz, U.; Lim, H.; Brodie, E. L.

2012-12-01

Pelosinus species are fermentative firmicutes that were recently reported to be prominent members of microbial communities at contaminated subsurface sites in multiple locations. Here we report metabolic characteristics and their putative genetic basis in Pelosinus sp. strain HCF1, an isolate that predominated anaerobic, Cr(VI)-reducing columns constructed with Hanford 100H aquifer sediment (constituting 80% of the total bacterial population in the columns). Strain HCF1 ferments lactate to propionate and acetate (a complete fermentation pathway was identified in the genome) and its genome encodes both [NiFe]- and [FeFe]-hydrogenases for H2 cycling. This bacterium has unexpected capabilities and gene content associated with reduction of nitrogen oxides. In this strain, either H2 or lactate can act as a sole electron donor for nitrate, Cr(VI), and Fe(III) reduction. Transcriptional studies demonstrated differential expression of nitrate reductases and hydrogenases. Overall, the unexpected metabolic capabilities and gene content reported here broaden our perspective on what biogeochemical and ecological roles this species might play as a prominent member of microbial communities in subsurface environments.

Polyphenol-rich sorghum brans alter colon microbiota and impact species diversity and species richness after multiple bouts of dextran sodium sulfate-induced colitis.

PubMed

Ritchie, Lauren E; Sturino, Joseph M; Carroll, Raymond J; Rooney, Lloyd W; Azcarate-Peril, M Andrea; Turner, Nancy D

2015-03-01

The microbiota affects host health, and dysbiosis is involved in colitis. Sorghum bran influences butyrate concentrations during dextran sodium sulfate (DSS) colitis, suggesting microbiota changes. We aimed to characterize the microbiota during colitis, and ascertain if polyphenol-rich sorghum bran diets mitigate these effects. Rats (n = 80) were fed diets containing 6% fiber from cellulose, or Black (3-deoxyanthocyanins), Sumac (condensed tannins), or Hi Tannin black (both) sorghum bran. Inflammation was induced three times using 3% DSS for 48 h (40 rats, 2 week separation), and the microbiota characterized by pyrosequencing. The Firmicutes/Bacteroidetes ratio was higher in Cellulose DSS rats. Colonic injury negatively correlated with Firmicutes, Actinobacteria, Lactobacillales and Lactobacillus, and positively correlated with Unknown/Unclassified. Post DSS#2, richness was significantly lower in Sumac and Hi Tannin black. Post DSS#3 Bacteroidales, Bacteroides, Clostridiales, Lactobacillales and Lactobacillus were reduced, with no Clostridium identified. Diet significantly affected Bacteroidales, Bacteroides, Clostridiales and Lactobacillus post DSS#2 and #3. Post DSS#3 diet significantly affected all genus, including Bacteroides and Lactobacillus, and diversity and richness increased. Sumac and Hi Tannin black DSS had significantly higher richness compared to controls. Thus, these sorghum brans may protect against alterations observed during colitis including reduced microbial diversity and richness, and dysbiosis of Firmicutes/Bacteroidetes. © FEMS 2015. All rights reserved. For permissions, please e-mail: journals.permissions@oup.com.

Diverse bacteria isolated from microtherm oil-production water.

PubMed

Sun, Ji-Quan; Xu, Lian; Zhang, Zhao; Li, Yan; Tang, Yue-Qin; Wu, Xiao-Lei

2014-02-01

In total, 435 pure bacterial strains were isolated from microtherm oil-production water from the Karamay Oilfield, Xinjiang, China, by using four media: oil-production water medium (Cai medium), oil-production water supplemented with mineral salt medium (CW medium), oil-production water supplemented with yeast extract medium (CY medium), and blood agar medium (X medium). The bacterial isolates were affiliated with 61 phylogenetic groups that belong to 32 genera in the phyla Actinobacteria, Firmicutes, and Proteobacteria. Except for the Rhizobium, Dietzia, and Pseudomonas strains that were isolated using all the four media, using different media led to the isolation of bacteria with different functions. Similarly, nonheme diiron alkane monooxygenase genes (alkB/alkM) also clustered according to the isolation medium. Among the bacterial strains, more than 24 % of the isolates could use n-hexadecane as the sole carbon source for growth. For the first time, the alkane-degrading ability and alkB/alkM were detected in Rhizobium, Rhodobacter, Trichococcus, Micrococcus, Enterococcus, and Bavariicoccus strains, and the alkM gene was detected in Firmicutes strains.

High nutrient transport and cycling potential revealed in the microbial metagenome of Australian sea lion (Neophoca cinerea) faeces.

PubMed

Lavery, Trish J; Roudnew, Ben; Seymour, Justin; Mitchell, James G; Jeffries, Thomas

2012-01-01

Metagenomic analysis was used to examine the taxonomic diversity and metabolic potential of an Australian sea lion (Neophoca cinerea) gut microbiome. Bacteria comprised 98% of classifiable sequences and of these matches to Firmicutes (80%) were dominant, with Proteobacteria and Actinobacteria representing 8% and 2% of matches respectively. The relative proportion of Firmicutes (80%) to Bacteriodetes (2%) is similar to that in previous studies of obese humans and obese mice, suggesting the gut microbiome may confer a predisposition towards the excess body fat that is needed for thermoregulation within the cold oceanic habitats foraged by Australian sea lions. Core metabolic functions, including carbohydrate utilisation (14%), protein metabolism (9%) and DNA metabolism (7%) dominated the metagenome, but in comparison to human and fish gut microbiomes there was a significantly higher proportion of genes involved in phosphorus metabolism (2.4%) and iron scavenging mechanisms (1%). When sea lions defecate at sea, the relatively high nutrient metabolism potential of bacteria in their faeces may accelerate the dissolution of nutrients from faecal particles, enhancing their persistence in the euphotic zone where they are available to stimulate marine production.

Ketide Synthase (KS) Domain Prediction and Analysis of Iterative Type II PKS Gene in Marine Sponge-Associated Actinobacteria Producing Biosurfactants and Antimicrobial Agents

PubMed Central

Selvin, Joseph; Sathiyanarayanan, Ganesan; Lipton, Anuj N.; Al-Dhabi, Naif Abdullah; Valan Arasu, Mariadhas; Kiran, George S.

2016-01-01

The important biological macromolecules, such as lipopeptide and glycolipid biosurfactant producing marine actinobacteria were analyzed and their potential linkage between type II polyketide synthase (PKS) genes was explored. A unique feature of type II PKS genes is their high amino acid (AA) sequence homology and conserved gene organization. These enzymes mediate the biosynthesis of polyketide natural products with enormous structural complexity and chemical nature by combinatorial use of various domains. Therefore, deciphering the order of AA sequence encoded by PKS domains tailored the chemical structure of polyketide analogs still remains a great challenge. The present work deals with an in vitro and in silico analysis of PKS type II genes from five actinobacterial species to correlate KS domain architecture and structural features. Our present analysis reveals the unique protein domain organization of iterative type II PKS and KS domain of marine actinobacteria. The findings of this study would have implications in metabolic pathway reconstruction and design of semi-synthetic genomes to achieve rational design of novel natural products. PMID:26903957

Functional gene-based discovery of phenazines from the actinobacteria associated with marine sponges in the South China Sea.

PubMed

Karuppiah, Valliappan; Li, Yingxin; Sun, Wei; Feng, Guofang; Li, Zhiyong

2015-07-01

Phenazines represent a large group of nitrogen-containing heterocyclic compounds produced by the diverse group of bacteria including actinobacteria. In this study, a total of 197 actinobacterial strains were isolated from seven different marine sponge species in the South China Sea using five different culture media. Eighty-seven morphologically different actinobacterial strains were selected and grouped into 13 genera, including Actinoalloteichus, Kocuria, Micrococcus, Micromonospora, Mycobacterium, Nocardiopsis, Prauserella, Rhodococcus, Saccharopolyspora, Salinispora, Serinicoccus, and Streptomyces by the phylogenetic analysis of 16S rRNA gene. Based on the screening of phzE genes, ten strains, including five Streptomyces, two Nocardiopsis, one Salinispora, one Micrococcus, and one Serinicoccus were found to be potential for phenazine production. The level of phzE gene expression was highly expressed in Nocardiopsis sp. 13-33-15, 13-12-13, and Serinicoccus sp. 13-12-4 on the fifth day of fermentation. Finally, 1,6-dihydroxy phenazine (1) from Nocardiopsis sp. 13-33-15 and 13-12-13, and 1,6-dimethoxy phenazine (2) from Nocardiopsis sp. 13-33-15 were isolated and identified successfully based on ESI-MS and NMR analysis. The compounds 1 and 2 showed antibacterial activity against Bacillus mycoides SJ14, Staphylococcus aureus SJ51, Escherichia coli SJ42, and Micrococcus luteus SJ47. This study suggests that the integrated approach of gene screening and chemical analysis is an effective strategy to find the target compounds and lays the basis for the production of phenazine from the sponge-associated actinobacteria.

Antibacterial and Antioxidant Activities of Novel Actinobacteria Strain Isolated from Gulf of Khambhat, Gujarat.

PubMed

Dholakiya, Riddhi N; Kumar, Raghawendra; Mishra, Avinash; Mody, Kalpana H; Jha, Bhavanath

2017-01-01

Bacterial secondary metabolites possess a wide range of biologically active compounds including antibacterial and antioxidants. In this study, a Gram-positive novel marine Actinobacteria was isolated from sea sediment which showed 84% 16S rRNA gene sequence (KT588655) similarity with Streptomyces variabilis (EU841661) and designated as Streptomyces variabilis RD-5. The genus Streptomyces is considered as a promising source of bioactive secondary metabolites. The isolated novel bacterial strain was characterized by antibacterial characteristics and antioxidant activities. The BIOLOG based analysis suggested that S. variabilis RD-5 utilized a wide range of substrates compared to the reference strain. The result is further supported by statistical analysis such as AWCD (average well color development), heat-map and PCA (principal component analysis). The whole cell fatty acid profiling showed the dominance of iso/anteiso branched C15-C17 long chain fatty acids. The identified strain S. variabilis RD-5 exhibited a broad spectrum of antibacterial activities for the Gram-negative bacteria ( Escherichia coli NCIM 2065, Shigella boydii NCIM, Klebsiella pneumoniae, Enterobacter cloacae, Pseudomonas sp. NCIM 2200 and Salmonella enteritidis NCIM), and Gram-positive bacteria ( Bacillus subtilis NCIM 2920 and Staphylococcus aureus MTCC 96). Extract of S. variabilis strain RD-5 showed 82.86 and 89% of 2,2-diphenyl-1-picrylhydrazyl (DPPH) free radical scavenging and metal chelating activity, respectively, at 5.0 mg/mL. While H 2 O 2 scavenging activity was 74.5% at 0.05 mg/mL concentration. Furthermore, polyketide synthases (PKSs types I and II), an enzyme complex that produces polyketides, the encoding gene(s) detected in the strain RD-5 which may probably involve for the synthesis of antibacterial compound(s). In conclusion, a novel bacterial strain of Actinobacteria , isolated from the unexplored sea sediment of Alang, Gulf of Khambhat (Gujarat), India showed promising

Antibacterial and Antioxidant Activities of Novel Actinobacteria Strain Isolated from Gulf of Khambhat, Gujarat

PubMed Central

Dholakiya, Riddhi N.; Kumar, Raghawendra; Mishra, Avinash; Mody, Kalpana H.; Jha, Bhavanath

2017-01-01

Bacterial secondary metabolites possess a wide range of biologically active compounds including antibacterial and antioxidants. In this study, a Gram-positive novel marine Actinobacteria was isolated from sea sediment which showed 84% 16S rRNA gene sequence (KT588655) similarity with Streptomyces variabilis (EU841661) and designated as Streptomyces variabilis RD-5. The genus Streptomyces is considered as a promising source of bioactive secondary metabolites. The isolated novel bacterial strain was characterized by antibacterial characteristics and antioxidant activities. The BIOLOG based analysis suggested that S. variabilis RD-5 utilized a wide range of substrates compared to the reference strain. The result is further supported by statistical analysis such as AWCD (average well color development), heat-map and PCA (principal component analysis). The whole cell fatty acid profiling showed the dominance of iso/anteiso branched C15–C17 long chain fatty acids. The identified strain S. variabilis RD-5 exhibited a broad spectrum of antibacterial activities for the Gram-negative bacteria (Escherichia coli NCIM 2065, Shigella boydii NCIM, Klebsiella pneumoniae, Enterobacter cloacae, Pseudomonas sp. NCIM 2200 and Salmonella enteritidis NCIM), and Gram-positive bacteria (Bacillus subtilis NCIM 2920 and Staphylococcus aureus MTCC 96). Extract of S. variabilis strain RD-5 showed 82.86 and 89% of 2,2-diphenyl-1-picrylhydrazyl (DPPH) free radical scavenging and metal chelating activity, respectively, at 5.0 mg/mL. While H2O2 scavenging activity was 74.5% at 0.05 mg/mL concentration. Furthermore, polyketide synthases (PKSs types I and II), an enzyme complex that produces polyketides, the encoding gene(s) detected in the strain RD-5 which may probably involve for the synthesis of antibacterial compound(s). In conclusion, a novel bacterial strain of Actinobacteria, isolated from the unexplored sea sediment of Alang, Gulf of Khambhat (Gujarat), India showed promising

Anti-phytopathogen potential of endophytic actinobacteria isolated from tomato plants (Lycopersicon esculentum) in southern Brazil, and characterization of Streptomyces sp. R18(6), a potential biocontrol agent.

PubMed

de Oliveira, Margaroni Fialho; da Silva, Mariana Germano; Van Der Sand, Sueli T

2010-09-01

Tomato plants (Lycopersicon esculentum) are highly susceptible to phytopathogen attack. The resulting intensive application of pesticides on tomato crops can affect the environment and health of humans and animals. The objective of this study was to select potential biocontrol agents among actinobacteria from tomato plants, in a search for alternative phytopathogen control. We evaluated 70 endophytic actinobacteria isolated from tomato plants in southern Brazil, testing their antimicrobial activity, siderophore production, indoleacetic acid production, and phosphate solubility. The actinomycete isolate with the highest antimicrobial potential was selected using the agar-well diffusion method, in order to optimize conditions for the production of compounds with antimicrobial activity. For this study, six growth media (starch casein-SC, ISP2, Bennett's, Sahin, Czapek-Dox, and TSB), three temperatures (25 degrees C, 30 degrees C, and 35 degrees C) and different pH were tested. Of the actinobacteria tested, 88.6% showed antimicrobial activity against at least one phytopathogen, 72.1% showed a positive reaction for indoleacetic acid production, 86.8% produced siderophores and 16.2% showed a positive reaction for phosphate solubility. Isolate R18(6) was selected due to its antagonistic activity against all phytopathogenic microorganisms tested in this study. The best conditions for production were observed in the SC medium, at 30 degrees C and pH 7.0. The isolate R18(6) showed close biochemical and genetic similarity to Streptomyces pluricolorescens. Copyright 2010 Elsevier Masson SAS. All rights reserved.

Carbonate-Dissolving Bacteria from ‘Miliolite’, a Bioclastic Limestone, from Gopnath, Gujarat, Western India

PubMed Central

Subrahmanyam, Gangavarapu; Vaghela, Ravi; Bhatt, Nilesh Pinakinprasad; Archana, Gattupalli

2012-01-01

In the present investigation, the abundance and molecular phylogeny of part of the culturable bacterial population involved in the dissolution of “miliolite”, a bioclastic limestone, from Gopnath, India, was studied. Carbonate-dissolving bacteria were isolated, enumerated and screened for their ability to dissolve miliolite. Amplified ribosomal DNA restriction analysis (ARDRA) indicated 14 operational taxonomic units (OTUs) to be distributed in 5 different clades at a similarity coefficient of 0.85. Then, 16S rRNA sequence analysis helped to decipher that the majority of carbonate-dissolving bacteria were affiliated to phyla Firmicutes (Families Bacillaceae and Staphylococcaceae) and Actinobacteria (Family Promicromonosporaceae) indicating their role in miliolite weathering. PMID:22446314

Salmonella enterica synthesizes 5,6-dimethylbenzimidazolyl-(DMB)-α-riboside. Why some Firmicutes do not require the canonical DMB activation system to synthesize adenosylcobalamin.

PubMed

Mattes, Theodoric A; Escalante-Semerena, Jorge C

2017-01-01

5,6-Dimethylbenzimidazolyl-(DMB)-α-ribotide [α-ribazole-5'-phosphate (α-RP)] is an intermediate in the biosynthesis of adenosylcobalamin (AdoCbl) in many prokaryotes. In such microbes, α-RP is synthesized by nicotinate mononucleotide (NaMN):DMB phosphoribosyltransferases (CobT in Salmonella enterica), in a reaction that is considered to be the canonical step for the activation of the base of the nucleotide present in adenosylcobamides. Some Firmicutes lack CobT-type enzymes but have a two-protein system comprised of a transporter (i.e., CblT) and a kinase (i.e., CblS) that can salvage exogenous α-ribazole (α-R) from the environment using CblT to take up α-R, followed by α-R phosphorylation by CblS. We report that Geobacillus kaustophilus CblT and CblS proteins restore α-RP synthesis in S. enterica lacking the CobT enzyme. We also show that a S. enterica cobT strain that synthesizes GkCblS ectopically makes only AdoCbl, even under growth conditions where the synthesis of pseudoCbl is favored. Our results indicate that S. enterica synthesizes α-R, a metabolite that had not been detected in this bacterium and that GkCblS has a strong preference for DMB-ribose over adenine-ribose as substrate. We propose that in some Firmicutes DMB is activated to α-RP via α-R using an as-yet-unknown route to convert DMB to α-R and CblS to convert α-R to α-RP. © 2016 John Wiley & Sons Ltd.

Microbiomes of the dust particles collected from the International Space Station and Spacecraft Assembly Facilities.

PubMed

Checinska, Aleksandra; Probst, Alexander J; Vaishampayan, Parag; White, James R; Kumar, Deepika; Stepanov, Victor G; Fox, George E; Nilsson, Henrik R; Pierson, Duane L; Perry, Jay; Venkateswaran, Kasthuri

2015-10-27

The International Space Station (ISS) is a unique built environment due to the effects of microgravity, space radiation, elevated carbon dioxide levels, and especially continuous human habitation. Understanding the composition of the ISS microbial community will facilitate further development of safety and maintenance practices. The primary goal of this study was to characterize the viable microbiome of the ISS-built environment. A second objective was to determine if the built environments of Earth-based cleanrooms associated with space exploration are an appropriate model of the ISS environment. Samples collected from the ISS and two cleanrooms at the Jet Propulsion Laboratory (JPL, Pasadena, CA) were analyzed by traditional cultivation, adenosine triphosphate (ATP), and propidium monoazide-quantitative polymerase chain reaction (PMA-qPCR) assays to estimate viable microbial populations. The 16S rRNA gene Illumina iTag sequencing was used to elucidate microbial diversity and explore differences between ISS and cleanroom microbiomes. Statistical analyses showed that members of the phyla Actinobacteria, Firmicutes, and Proteobacteria were dominant in the samples examined but varied in abundance. Actinobacteria were predominant in the ISS samples whereas Proteobacteria, least abundant in the ISS, dominated in the cleanroom samples. The viable bacterial populations seen by PMA treatment were greatly decreased. However, the treatment did not appear to have an effect on the bacterial composition (diversity) associated with each sampling site. The results of this study provide strong evidence that specific human skin-associated microorganisms make a substantial contribution to the ISS microbiome, which is not the case in Earth-based cleanrooms. For example, Corynebacterium and Propionibacterium (Actinobacteria) but not Staphylococcus (Firmicutes) species are dominant on the ISS in terms of viable and total bacterial community composition. The results obtained will

Proposal to designate the order Actinomycetales Buchanan 1917, 162 (Approved Lists 1980) as the nomenclatural type of the class Actinobacteria. Request for an Opinion

PubMed Central

2017-01-01

The name of the class Actinobacteria is illegitimate according to Rules 15, 22 and 27(3) because it was proposed without the designation of a nomenclatural type. I therefore propose to designate the order Actinomycetales Buchanan 1917, 162 (Approved Lists 1980) as its nomenclatural type, based on Rule 22 of the International Code of Nomenclature of Prokaryotes. PMID:28840812

Proposal to designate the order Actinomycetales Buchanan 1917, 162 (Approved Lists 1980) as the nomenclatural type of the class Actinobacteria. Request for an Opinion.

PubMed

Oren, Aharon

2017-09-01

The name of the class Actinobacteria is illegitimate according to Rules 15, 22 and 27(3) because it was proposed without the designation of a nomenclatural type. I therefore propose to designate the order Actinomycetales Buchanan 1917, 162 (Approved Lists 1980) as its nomenclatural type, based on Rule 22 of the International Code of Nomenclature of Prokaryotes.

Metagenomics uncovers a new group of low GC and ultra-small marine Actinobacteria

PubMed Central

Ghai, Rohit; Mizuno, Carolina Megumi; Picazo, Antonio; Camacho, Antonio; Rodriguez-Valera, Francisco

2013-01-01

We describe a deep-branching lineage of marine Actinobacteria with very low GC content (33%) and the smallest free living cells described yet (cell volume ca. 0.013 μm3), even smaller than the cosmopolitan marine photoheterotroph, ‘Candidatus Pelagibacter ubique'. These microbes are highly related to 16S rRNA sequences retrieved by PCR from the Pacific and Atlantic oceans 20 years ago. Metagenomic fosmids allowed a virtual genome reconstruction that also indicated very small genomes below 1 Mb. A new kind of rhodopsin was detected indicating a photoheterotrophic lifestyle. They are estimated to be ~4% of the total numbers of cells found at the site studied (the Mediterranean deep chlorophyll maximum) and similar numbers were estimated in all tropical and temperate photic zone metagenomes available. Their geographic distribution mirrors that of picocyanobacteria and there appears to be an association between these microbial groups. A new sub-class, ‘Candidatus Actinomarinidae' is proposed to designate these microbes. PMID:23959135

Comparison of bacterial community structures of terrestrial cyanobacterium Nostoc flagelliforme in three different regions of China using PCR-DGGE analysis.

PubMed

Han, Pei-pei; Shen, Shi-gang; Jia, Shi-ru; Wang, Hui-yan; Zhong, Cheng; Tan, Zhi-lei; Lv, He-xin

2015-07-01

Filamentous Nostoc flagelliforme form colloidal complex, with beaded cells interacting with other bacteria embedded in the complex multilayer sheath. However, the species of bacteria in the sheath and the interaction between N. flagelliforme and associated bacteria remain unclear. In this study, PCR-denaturing gradient gel electrophoresis (DGGE) was used to investigate the bacterial communities of N. flagelliforme from three regions of China. DGGE patterns showed variations in all samples, exhibiting 25 discrete bands with various intensities. The diversity index analysis of bands profiles suggested the high similarity of bacterial communities to each other but also the dependence of microbial composition on each location. Phylogenetic affiliation indicated that the majority of the sequences obtained were affiliated with Actinobacteria, Cyanobacteria, Proteobacteria, Acidobacteria, Bacteroidetes, of which Cyanobacteria was dominant, followed the Proteobacteria. Members of the genus Nostoc were the most abundant in all samples. Rhizobiales and Actinobacteria were identified, whereas, Craurococcus, Caulobacter, Pseudomonas, Terriglobus and Mucilaginibacter were also identified at low levels. Through comparing the bacterial composition of N. flagelliforme from different regions, it was revealed that N. flagelliforme could facilitate the growth of other microorganisms including both autotrophic bacteria and heterotrophic ones and positively contributed to their harsh ecosystems. The results indicated N. flagelliforme played an important role in diversifying the microbial community composition and had potential application in soil desertification.

Potential of semiarid soil from Caatinga biome as a novel source for mining lignocellulose-degrading enzymes.

PubMed

Lacerda Júnior, Gileno V; Noronha, Melline F; de Sousa, Sanderson Tarciso P; Cabral, Lucélia; Domingos, Daniela F; Sáber, Mírian L; de Melo, Itamar S; Oliveira, Valéria M

2017-02-01

The litterfall is the major organic material deposited in soil of Brazilian Caatinga biome, thus providing the ideal conditions for plant biomass-degrading microorganisms to thrive. Herein, the phylogenetic composition and lignocellulose-degrading capacity have been explored for the first time from a fosmid library dataset of Caatinga soil by sequence-based screening. A complex bacterial community dominated by Proteobacteria and Actinobacteria was unraveled. SEED subsystems-based annotations revealed a broad range of genes assigned to carbohydrate and aromatic compounds metabolism, indicating microbial ability to utilize plant-derived material. CAZy-based annotation identified 7275 genes encoding 37 glycoside hydrolases (GHs) families related to hydrolysis of cellulose, hemicellulose, oligosaccharides and other lignin-modifying enzymes. Taxonomic affiliation of genes showed high genetic potential of the phylum Acidobacteria for hemicellulose degradation, whereas Actinobacteria members appear to play an important role in celullose hydrolysis. Additionally, comparative analyses revealed greater GHs profile similarity among soils as compared to the digestive tract of animals capable of digesting plant biomass, particularly in the hemicellulases content. Combined results suggest a complex synergistic interaction of community members required for biomass degradation into fermentable sugars. This large repertoire of lignocellulolytic enzymes opens perspectives for mining potential candidates of biochemical catalysts for biofuels production from renewable resources and other environmental applications. © FEMS 2016. All rights reserved. For permissions, please e-mail: journals.permissions@oup.com.

The soil carbon/nitrogen ratio and moisture affect microbial community structures in alkaline permafrost-affected soils with different vegetation types on the Tibetan plateau.

PubMed

Zhang, Xinfang; Xu, Shijian; Li, Changming; Zhao, Lin; Feng, Huyuan; Yue, Guangyang; Ren, Zhengwei; Cheng, Guogdong

2014-01-01

In the Tibetan permafrost region, vegetation types and soil properties have been affected by permafrost degradation, but little is known about the corresponding patterns of their soil microbial communities. Thus, we analyzed the effects of vegetation types and their covariant soil properties on bacterial and fungal community structure and membership and bacterial community-level physiological patterns. Pyrosequencing and Biolog EcoPlates were used to analyze 19 permafrost-affected soil samples from four principal vegetation types: swamp meadow (SM), meadow (M), steppe (S) and desert steppe (DS). Proteobacteria, Acidobacteria, Bacteroidetes and Actinobacteria dominated bacterial communities and the main fungal phyla were Ascomycota, Basidiomycota and Mucoromycotina. The ratios of Proteobacteria/Acidobacteria decreased in the order: SM>M>S>DS, whereas the Ascomycota/Basidiomycota ratios increased. The distributions of carbon and nitrogen cycling bacterial genera detected were related to soil properties. The bacterial communities in SM/M soils degraded amines/amino acids very rapidly, while polymers were degraded rapidly by S/DS communities. UniFrac analysis of bacterial communities detected differences among vegetation types. The fungal UniFrac community patterns of SM differed from the others. Redundancy analysis showed that the carbon/nitrogen ratio had the main effect on bacteria community structures and their diversity in alkaline soil, whereas soil moisture was mainly responsible for structuring fungal communities. Thus, microbial communities and their functioning are probably affected by soil environmental change in response to permafrost degradation. Copyright © 2014 Institut Pasteur. Published by Elsevier Masson SAS. All rights reserved.

Effect of Saccharomyces boulardii and Mode of Delivery on the Early Development of the Gut Microbial Community in Preterm Infants

PubMed Central

Zeber-Lubecka, Natalia; Kulecka, Maria; Ambrozkiewicz, Filip; Paziewska, Agnieszka; Lechowicz, Milosz; Konopka, Ewa; Majewska, Urszula; Borszewska-Kornacka, Maria; Mikula, Michal; Cukrowska, Bozena; Ostrowski, Jerzy

2016-01-01

Background Recent advances in culture-independent approaches have enabled insights into the diversity, complexity, and individual variability of gut microbial communities. Objectives To examine the effect of oral administration of Saccharomyces (S.) boulardii and mode of delivery on the intestinal microbial community in preterm infants. Study Design Stool samples were collected from preterm newborns randomly divided into two groups: a probiotic-receiving group (n = 18) or a placebo group (n = 21). Samples were collected before probiotic intake (day 0), and after 2 and 6 weeks of supplementation. The composition of colonizing bacteria was assessed by 16S ribosomal RNA (rRNA) gene sequencing of fecal samples using the Ion 16S Metagenomics Kit and the Ion Torrent Personal Genome Machine platform. Results A total of 11932257 reads were generated, and were clustered into 459, 187, and 176 operational taxonomic units at 0 days, 2 weeks, and 6 weeks, respectively. Of the 17 identified phyla, Firmicutes Actinobacteria, Proteobacteria, and Bacteroidetes were universal. The microbial community differed at day 0 compared with at 2 weeks and 6 weeks. There was a tendency for increased bacterial diversity at 2 weeks and 6 weeks compared with day 0, and infants with a gestational age of 31 weeks or higher presented increased bacterial diversity prior to S. boulardii administration. Firmicutes and Proteobacteria remained stable during the observation period, whereas Actinobacteria and Bacteroidetes increased in abundance, the latter particularly more sharply in vaginally delivered infants. Conclusion While the mode of delivery may influence the development of a microbial community, this study had not enough power to detect statistical differences between cohorts supplemented with probiotics, and in a consequence, to speculate on S. boulardii effect on gut microbiome composition in preterm newborns. PMID:26918330

Comparison of Microbial Communities in Swine Manure at Various Temperatures and storage times.

PubMed

Lim, Joung-Soo; Yang, Seung Hak; Kim, Bong-Soo; Lee, Eun Young

2018-01-26

This study was designed to investigate the effects of temperature and storage time on the evolution of bacterial communities in swine manure. Manure was stored at -20°C, 4°C, 20°C, or 37°C and sampled at 7-day intervals over 28 days of storage, for a total of 5 time points. To assess the bacterial species present, 16S ribosomal RNA gene sequences were analyzed using pyrosequencing. After normalization, 113,934 sequence reads were obtained, with an average length of 466.6 ± 4.4 bp. The diversity indices of the communities reduced as temperature and storage time increased, and the slopes of rarefaction curves decreased from the second week in samples stored at -20 °C and 4 °C. These results indicate that the richness of the bacterial community in the manure reduced as temperature and storage time increased. Firmicutes were the dominant phylum in all samples examined, ranging from 89.3% to 98.8% of total reads, followed by Actinobacteria, which accounted for 0.6% to 7.9%. A change in community composition was observed in samples stored at 37 °C during the first 7 days, indicating that temperature plays an important role in determining the microbiota of swine manure. Clostridium, Turicibacter, Streptococcus, and Lactobacillus within Firmicutes, and Corynebacterium within Actinobacteria were the most dominant genera in fresh manure and all stored samples. Based on our findings, we propose Clostridium as an indicator genus of swine manure decomposition in an anaerobic environment. The proportions of dominant genera changed in samples stored at 20 °C and 37 °C during the fourth week. Based on these results, it was concluded that the microbial communities of swine manure change rapidly as storage time and temperature increase.

Age-Related Variations in Intestinal Microflora of Free-Range and Caged Hens.

PubMed

Cui, Yizhe; Wang, Qiuju; Liu, Shengjun; Sun, Rui; Zhou, Yaqiang; Li, Yue

2017-01-01

Free range feeding pattern puts the chicken in a mixture of growth materials and enteric bacteria excreted by nature, while it is typically unique condition materials and enteric bacteria in commercial caged hens production. Thus, the gastrointestinal microflora in two feeding patterns could be various. However, it remains poorly understood how feeding patterns affect development and composition of layer hens' intestinal microflora. In this study, the effect of feeding patterns on the bacteria community in layer hens' gut was investigated using free range and caged feeding form. Samples of whole small intestines and cecal digesta were collected from young hens (8-weeks) and mature laying hens (30-weeks). Based on analysis using polymerase chain reaction-denaturing gradient gel electrophoresis and sequencing of bacterial 16S rDNA gene amplicons, the microflora of all intestinal contents were affected by both feeding patterns and age of hens. Firmicutes, Bacteroidetes, Actinobacteria, Proteobacteria, and Fusobacteria were the main components. Additionally, uncultured environmental samples were found too. There were large differences between young hens and adult laying hens, the latter had more Firmicutes and Bacteroidetes, and bacterial community is more abundant in 30-weeks laying hens of all six phyla than 8-weeks young hens of only two phyla. In addition, the differences were also observed between free range and caged hens. Free range hens had richer Actinobacteria, Bacteroidetes, and Proteobacteria. Most of strains found were detected more abundant in small intestines than in cecum. Also the selected Lactic acid bacteria from hens gut were applied in feed and they had beneficial effects on growth performance and jejunal villus growth of young broilers. This study suggested that feeding patterns have an importance effect on the microflora composition of hens, which may impact the host nutritional status and intestinal health.

Cultivation Versus Molecular Analysis of Banana (Musa sp.) Shoot-Tip Tissue Reveals Enormous Diversity of Normally Uncultivable Endophytic Bacteria.

PubMed

Thomas, Pious; Sekhar, Aparna Chandra

2017-05-01

The interior of plants constitutes a unique environment for microorganisms with various organisms inhabiting as endophytes. Unlike subterranean plant parts, aboveground parts are relatively less explored for endophytic microbial diversity. We employed a combination of cultivation and molecular approaches to study the endophytic bacterial diversity in banana shoot-tips. Cultivable bacteria from 20 sucker shoot-tips of cv. Grand Naine included 37 strains under 16 genera and three phyla (Proteobacteria, Actinobacteria, Firmicutes). 16S rRNA gene-ribotyping approach on 799f and 1492r PCR-amplicons to avoid plant organelle sequences was ineffective showing limited bacterial diversity. 16S rRNA metagene profiling targeting the V3-V4 hypervariable region after filtering out the chloroplast (74.2 %), mitochondrial (22.9 %), and unknown sequences (1.1 %) revealed enormous bacterial diversity. Proteobacteria formed the predominant phylum (64 %) succeeded by Firmicutes (12.1 %), Actinobacteria (9.5 %), Bacteroidetes (6.4 %), Planctomycetes, Cyanobacteria, and minor shares (<1 %) of 14 phyla including several candidate phyla besides the domain Euryarchaeota (0.2 %). Microbiome analysis of single shoot-tips through 16S rRNA V3 region profiling showed similar taxonomic richness and diversity and was less affected by plant sequence interferences. DNA extraction kit ominously influenced the phylogenetic diversity. The study has revealed vast diversity of normally uncultivable endophytic bacteria prevailing in banana shoot-tips (20 phyla, 46 classes) with about 2.6 % of the deciphered 269 genera and 1.5 % of the 656 observed species from the same source of shoot-tips attained through cultivation. The predominant genera included several agriculturally important bacteria. The study reveals an immense ecosystem of endophytic bacteria in banana shoot tissues endorsing the earlier documentation of intracellular "Cytobacts" and "Peribacts" with possible roles in plant

Comparison among the microbial communities in the lake, lake wetland, and estuary sediments of a plain river network.

PubMed

Huang, Wei; Chen, Xing; Wang, Kun; Chen, Junyi; Zheng, Binghui; Jiang, Xia

2018-06-10

Sediment microbial communities from plain river networks exert different effects on pollutant transformation and migration in lake basins. In this study, we examined millions of Illumina reads (16S rRNA gene amplicons) to compare lake, lake wetland, and estuary bacterial communities through a technically consistent approach. Results showed that bacterial communities in the sampled lake sediments had the highest alpha-diversity (Group B), than in sampled lake wetland sediments and estuary sediments. Proteobacteria was the most abundant (more than 30%) phyla in all the sediments. The lake sediments had more Nitrospirae (1.63%-11.75%) and Acidobacteria (3.46%-10.21%) than the lake wetland and estuary sediments, and estuary sediments had a greater abundance of the phylum Firmicutes (mean of 22.30%). Statistical analysis (LEfSe) revealed that lake wetland sediments contained greater abundances of the class Anaerolineaceae, orders Xanthomonadales, Pseudomonadales, and genera Flavobacterium, Acinetobacter. The lake sediments had a distinct community of diverse primary producers, such as phylum Acidobacteria, order Ignavibacteriales, and families Nitrospiraceae, Hydrogenophilaceae. Total phosphorus and organic matter were the main factors influencing the bacterial communities in sediments from several parts of the lake wetland and river estuary (p < .05). The novel insights into basin pollution control in plain river networks may be obtained from microbial distribution in sediments from different basin regions. © 2018 The Authors. MicrobiologyOpen published by John Wiley & Sons Ltd.

Actinobacteria consortium as an efficient biotechnological tool for mixed polluted soil reclamation: Experimental factorial design for bioremediation process optimization.

PubMed

Aparicio, Juan Daniel; Raimondo, Enzo Emanuel; Gil, Raúl Andrés; Benimeli, Claudia Susana; Polti, Marta Alejandra

2018-01-15

The objective of the present work was to establish optimal biological and physicochemical parameters in order to remove simultaneously lindane and Cr(VI) at high and/or low pollutants concentrations from the soil by an actinobacteria consortium formed by Streptomyces sp. M7, MC1, A5, and Amycolatopsis tucumanensis AB0. Also, the final aim was to treat real soils contaminated with Cr(VI) and/or lindane from the Northwest of Argentina employing the optimal biological and physicochemical conditions. In this sense, after determining the optimal inoculum concentration (2gkg -1 ), an experimental design model with four factors (temperature, moisture, initial concentration of Cr(VI) and lindane) was employed for predicting the system behavior during bioremediation process. According to response optimizer, the optimal moisture level was 30% for all bioremediation processes. However, the optimal temperature was different for each situation: for low initial concentrations of both pollutants, the optimal temperature was 25°C; for low initial concentrations of Cr(VI) and high initial concentrations of lindane, the optimal temperature was 30°C; and for high initial concentrations of Cr(VI), the optimal temperature was 35°C. In order to confirm the model adequacy and the validity of the optimization procedure, experiments were performed in six real contaminated soils samples. The defined actinobacteria consortium reduced the contaminants concentrations in five of the six samples, by working at laboratory scale and employing the optimal conditions obtained through the factorial design. Copyright © 2017 Elsevier B.V. All rights reserved.

Halophilic & halotolerant prokaryotes in humans.

PubMed

Seck, El Hadji; Dufour, Jean-Charles; Raoult, Didier; Lagier, Jean-Christophe

2018-05-04

Halophilic prokaryotes are described as microorganisms living in hypersaline environments. Here, we list the halotolerant and halophilic bacteria which have been isolated in humans. Of the 52 halophilic prokaryotes, 32 (61.54%) were moderately halophilic, 17 (32.69%) were slightly halophilic and three (5.76%) were extremely halophilic prokaryotes. At the phylum level, 29 (54.72%) belong to Firmicutes, 15 (28.84%) to Proteobacteria, four (7.69%) to Actinobacteria, three (5.78%) to Euryarchaeota and one (1.92%) belongs to Bacteroidetes. Halophilic prokaryotes are rarely pathogenic: of these 52 halophilic prokaryotes only two (3.92%) species were classified in Risk Group 2 (Vibrio cholerae, Vibrio parahaemolyticus) and one (1.96%), species in Risk Group 3 (Bacillus anthracis).

Identification and bioactive potential of marine microorganisms from selected Florida coastal areas.

PubMed

Christensen, Anna; Martin, Glenroy D A

2017-08-01

The ocean, with its rich untapped chemical biodiversity, continues to serve as a source of potentially new therapeutic agents. The evaluation of the diversity of cultivable microorganisms from the marine sponge Halichondria panicea and ocean sediment samples were examined and their potential as sources of antimicrobial and antiproliferative agents were investigated. The marine sponge and sediments were collected at different depths (0.9-6 meters) and locations in Florida, including Florida Keys, Port St. Joe in Pensacola, Pensacola Bay, Pensacola Beach, and Fort Pickens. Twenty-one cultivatable isolates were grouped according to their morphology and identified using 16S rRNA molecular taxonomy. The bacterial community identified consisted of members belonging to the Actinobacteria, Bacteroidetes, Proteobacteria (Alpha- and Gamma-classes) and Firmicutes phylogeny. Seven of the microbes exhibited mild to significant cytotoxic activities against five microbial indicators but no significant cytotoxic activities were observed against the pancreatic (PANC-1) nor the multidrug-resistant ovarian cancer cell lines (NCI/ADR). This work reaffirms the phyla Actinobacteria and Proteobacteria as sources of potential bioactive natural product candidates for drug discovery and development. © 2017 The Authors. MicrobiologyOpen published by John Wiley & Sons Ltd.

Bacterium-bacterium inhibitory interactions among psychrotrophic bacteria isolated from Antarctic seawater (Terra Nova Bay, Ross Sea).

PubMed

Lo Giudice, Angelina; Brilli, Matteo; Bruni, Vivia; De Domenico, Maria; Fani, Renato; Michaud, Luigi

2007-06-01

One hundred and forty bacteria isolated from Antarctic seawater samples were examined for their ability to inhibit the growth of indigenous isolates and their sensitivity to antibacterial activity expressed by one another. On the basis of 16S rRNA gene sequencing and analysis, bacterial isolates were assigned to five phylogenetically different taxa, Actinobacteria, alpha and gamma subclasses of Proteobacteria, Bacillaceae, and Bacteroidetes. Twenty-one isolates (15%), predominantly Actinobacteria, exhibited antagonistic properties against marine bacteria of Antarctic origin. Members of Bacteroidetes and Firmicutes did not show any inhibitory activity. Differences were observed among inhibition patterns of single isolates, suggesting that their activity was more likely strain-specific rather than dependent on phylogenetic affiliation. A novel analysis based on network theory confirmed these results, showing that the structure of this population is probably robust to perturbations, but also that it depends strongly on the most active strains. The determination of plasmid incidence in the bacterial strains investigated revealed that there was no correlation between their presence and the antagonistic activity. The data presented here provide evidence for the antagonistic interactions within bacterial strains inhabiting Antarctic seawater and suggest the potential exploitation of Antarctic bacteria as a novel source of antibiotics.

Acidithrix ferrooxidans gen. nov., sp. nov.; a filamentous and obligately heterotrophic, acidophilic member of the Actinobacteria that catalyzes dissimilatory oxido-reduction of iron.

PubMed

Jones, Rose M; Johnson, D Barrie

2015-01-01

A novel acidophilic member of the phylum Actinobacteria was isolated from an acidic stream draining an abandoned copper mine in north Wales. The isolate (PY-F3) was demonstrated to be a heterotroph that catalyzed the oxidation of ferrous iron (but not of sulfur or hydrogen) under aerobic conditions, and the reduction of ferric iron under micro-aerobic and anaerobic conditions. PY-F3 formed long entangled filaments of cells (>50 μm long) during active growth phases, though these degenerated into smaller fragments and single cells in late stationary phase. Although isolate PY-F3 was not observed to grow below pH 2.0 and 10 °C, harvested biomass was found to oxidize ferrous iron at relatively fast rates at pH 1.5 and 5 °C. Phylogenetic analysis, based on comparisons of 16S rRNA gene sequences, showed that isolate PY-F3 has 91-93% gene similarity to those of the four classified genera and species of acidophilic Actinobacteria, and therefore is a representative of a novel genus. The binomial Acidithrix ferrooxidans is proposed for this new species, with PY-F3 as the designated type strain (=DSM 28176(T), =JCM 19728(T)). Copyright © 2015 Institut Pasteur. Published by Elsevier Masson SAS. All rights reserved.

High Nutrient Transport and Cycling Potential Revealed in the Microbial Metagenome of Australian Sea Lion (Neophoca cinerea) Faeces

PubMed Central

Lavery, Trish J.; Roudnew, Ben; Seymour, Justin; Mitchell, James G.; Jeffries, Thomas

2012-01-01

Metagenomic analysis was used to examine the taxonomic diversity and metabolic potential of an Australian sea lion (Neophoca cinerea) gut microbiome. Bacteria comprised 98% of classifiable sequences and of these matches to Firmicutes (80%) were dominant, with Proteobacteria and Actinobacteria representing 8% and 2% of matches respectively. The relative proportion of Firmicutes (80%) to Bacteriodetes (2%) is similar to that in previous studies of obese humans and obese mice, suggesting the gut microbiome may confer a predisposition towards the excess body fat that is needed for thermoregulation within the cold oceanic habitats foraged by Australian sea lions. Core metabolic functions, including carbohydrate utilisation (14%), protein metabolism (9%) and DNA metabolism (7%) dominated the metagenome, but in comparison to human and fish gut microbiomes there was a significantly higher proportion of genes involved in phosphorus metabolism (2.4%) and iron scavenging mechanisms (1%). When sea lions defecate at sea, the relatively high nutrient metabolism potential of bacteria in their faeces may accelerate the dissolution of nutrients from faecal particles, enhancing their persistence in the euphotic zone where they are available to stimulate marine production. PMID:22606263

High Frequency and Diversity of Antimicrobial Activities Produced by Nasal Staphylococcus Strains against Bacterial Competitors

PubMed Central

Janek, Daniela; Zipperer, Alexander; Kulik, Andreas; Krismer, Bernhard; Peschel, Andreas

2016-01-01

The human nasal microbiota is highly variable and dynamic often enclosing major pathogens such as Staphylococcus aureus. The potential roles of bacteriocins or other mechanisms allowing certain bacterial clones to prevail in this nutrient-poor habitat have hardly been studied. Of 89 nasal Staphylococcus isolates, unexpectedly, the vast majority (84%) was found to produce antimicrobial substances in particular under habitat-specific stress conditions, such as iron limitation or exposure to hydrogen peroxide. Activity spectra were generally narrow but highly variable with activities against certain nasal members of the Actinobacteria, Proteobacteria, Firmicutes, or several groups of bacteria. Staphylococcus species and many other Firmicutes were insusceptible to most of the compounds. A representative bacteriocin was identified as a nukacin-related peptide whose inactivation reduced the capacity of the producer Staphylococcus epidermidis IVK45 to limit growth of other nasal bacteria. Of note, the bacteriocin genes were found on mobile genetic elements exhibiting signs of extensive horizontal gene transfer and rearrangements. Thus, continuously evolving bacteriocins appear to govern bacterial competition in the human nose and specific bacteriocins may become important agents for eradication of notorious opportunistic pathogens from human microbiota. PMID:27490492

Correlation between diet and gut bacteria in a population of young adults.

PubMed

Mayorga Reyes, Lino; González Vázquez, Raquel; Cruz Arroyo, Schahrasad M; Melendez Avalos, Araceli; Reyes Castillo, Pedro A; Chavaro Pérez, David A; Ramos Terrones, Idalia; Ramos Ibáñez, Norma; Rodríguez Magallanes, Magdalena M; Langella, Philippe; Bermúdez Humarán, Luis; Azaola Espinosa, Alejandro

2016-06-01

Dietary habits strongly influence gut microbiota. The aim of this study was to compare and correlated the abundance of Firmicutes and Bacteroidetes phyla, some representative bacteria of these phyla such as Bacteroides thetaiotaomicron, Prevotella, Faecalibacterium prausnitzii, Clostridium leptum and Bifidobacterium longum as a member of Actinobacteria phylum in young adults with their food intake. Faecal samples used came from lean subjects (BMI = 19.83 ± 0.94 kg/m(2)), overweight (BMI = 27.17 ± 0.51 kg/m(2)) and obese (BMI = 41.33 ± 5.25 kg/m(2)). There were significant differences in total studied gut microbiota between the overweight and lean groups. Members of the Firmicutes phylum, and Bifidobacterium longum, were more abundant in the lean group. The results suggest that diet rich in unsaturated fatty acids and fibre promote an abundant population of beneficial bacteria such as B. longum and Bacteroidetes. However, it has been considered that the results may be biased due to the size of the individuals studied; therefore the results could be only valid for the studied population.

Intestinal microbiota of healthy and unhealthy Atlantic salmon Salmo salar L. in a recirculating aquaculture system

NASA Astrophysics Data System (ADS)

Wang, Chun; Sun, Guoxiang; Li, Shuangshuang; Li, Xian; Liu, Ying

2017-04-01

The present study sampled the intestinal content of healthy and unhealthy Atlantic salmon (Salmo salar L.), the ambient water of unhealthy fish, and the biofilter material in the recirculating aquaculture system (RAS) to understand differences in the intestinal microbiota. The V4-V5 regions of the prokaryotic 16S rRNA genes in the samples were analyzed by MiSeq high-throughput sequencing. The fish were adults with no differences in body length or weight. Representative members of the intestinal microbiota were identified. The intestinal microbiota of the healthy fish included Proteobacteria (44.33%), Actinobacteria (17.89%), Bacteroidetes (15.25%), and Firmicutes (9.11%), among which the families Micrococcaceae and Oxalobacteraceae and genera Sphingomonas, Streptomyces, Pedobacter, Janthinobacterium, Burkholderia, and Balneimonas were most abundant. Proteobacteria (70.46%), Bacteroidetes (7.59%), and Firmicutes (7.55%) dominated the microbiota of unhealthy fish, and Chloroflexi (2.71%), and Aliivibrio and Vibrio as well as genera in the family Aeromonadaceae were most strongly represented. Overall, the intestinal hindgut microbiota differed between healthy and unhealthy fish. This study offers a useful tool for monitoring the health status of fish and for screening the utility of probiotics by studying the intestinal microbiota.

The gut microbiota in larvae of the housefly Musca domestica and their horizontal transfer through feeding.

PubMed

Zhao, Yao; Wang, Wanqiang; Zhu, Fen; Wang, Xiaoyun; Wang, Xiaoping; Lei, Chaoliang

2017-12-01

House fly larvae provide a prolific and sustainable source of proteins used in poultry and fish feed. Wheat bran is a superior diet for house fly larvae and has been widely investigated to exploit its potential in the food and feed area. Using Illumina MiSeq 16S rDNA sequencing, this study investigated the gut microbiota of house fly larvae feeding on wheat bran and the bacterial community in the wheat bran. The bacterial communities in the house fly larvae were dominated by the phyla Proteobacteria and Firmicutes. Enterobacteriaceae and Providencia were the predominant bacteria at the family and genus levels, respectively. Some bacteria in the phyla Actinobacteria, Proteobacteria, Bacteroidetes and Firmicutes may be transferred from the gut of house flies to the wheat bran during feeding and may be involved in degrading and utilizing polysaccharides in the cell wall of wheat bran. The significance of the gut microbiota of house fly larvae, their transferring and roles in degradation of wheat bran is discussed. These findings regarding the gut microbiota of house fly larvae will provide opportunities for research on the impact of microbial communities on poultry and fish.

Antimicrobial Activities of Bacteria Associated with the Brown Alga Padina pavonica

PubMed Central

Ismail, Amel; Ktari, Leila; Ahmed, Mehboob; Bolhuis, Henk; Boudabbous, Abdellatif; Stal, Lucas J.; Cretoiu, Mariana Silvia; El Bour, Monia

2016-01-01

Macroalgae belonging to the genus Padina are known to produce antibacterial compounds that may inhibit growth of human- and animal pathogens. Hitherto, it was unclear whether this antibacterial activity is produced by the macroalga itself or by secondary metabolite producing epiphytic bacteria. Here we report antibacterial activities of epiphytic bacteria isolated from Padina pavonica (Peacocks tail) located on northern coast of Tunisia. Eighteen isolates were obtained in pure culture and tested for antimicrobial activities. Based on the 16S rRNA gene sequences the isolates were closely related to Proteobacteria (12 isolates; 2 Alpha- and 10 Gammaproteobacteria), Firmicutes (4 isolates) and Actinobacteria (2 isolates). The antimicrobial activity was assessed as inhibition of growth of 12 species of pathogenic bacteria (Aeromonas salmonicida, A. hydrophila, Enterobacter xiangfangensis, Enterococcus faecium, Escherichia coli, Micrococcus sp., Salmonella typhimurium, Staphylococcus aureus, Streptococcus sp., Vibrio alginoliticus, V. proteolyticus, V. vulnificus) and one pathogenic yeast (Candida albicans). Among the Firmicutes, isolate P8, which is closely related to Bacillus pumilus, displayed the largest spectrum of growth inhibition of the pathogenic bacteria tested. The results emphasize the potential use of P. pavonica associated antagonistic bacteria as producers of novel antibacterial compounds. PMID:27462308

Intestinal microbiota of healthy and unhealthy Atlantic salmon Salmo salar L. in a recirculating aquaculture system

NASA Astrophysics Data System (ADS)

Wang, Chun; Sun, Guoxiang; Li, Shuangshuang; Li, Xian; Liu, Ying

2018-03-01

The present study sampled the intestinal content of healthy and unhealthy Atlantic salmon ( Salmo salar L.), the ambient water of unhealthy fish, and the biofilter material in the recirculating aquaculture system (RAS) to understand differences in the intestinal microbiota. The V4-V5 regions of the prokaryotic 16S rRNA genes in the samples were analyzed by MiSeq high-throughput sequencing. The fish were adults with no differences in body length or weight. Representative members of the intestinal microbiota were identified. The intestinal microbiota of the healthy fish included Proteobacteria (44.33%), Actinobacteria (17.89%), Bacteroidetes (15.25%), and Firmicutes (9.11%), among which the families Micrococcaceae and Oxalobacteraceae and genera Sphingomonas, Streptomyces, Pedobacter, Janthinobacterium, Burkholderia, and Balneimonas were most abundant. Proteobacteria (70.46%), Bacteroidetes (7.59%), and Firmicutes (7.55%) dominated the microbiota of unhealthy fish, and Chloroflexi (2.71%), and Aliivibrio and Vibrio as well as genera in the family Aeromonadaceae were most strongly represented. Overall, the intestinal hindgut microbiota differed between healthy and unhealthy fish. This study offers a useful tool for monitoring the health status of fish and for screening the utility of probiotics by studying the intestinal microbiota.

T box riboswitches in Actinobacteria: Translational regulation via novel tRNA interactions

PubMed Central

Sherwood, Anna V.; Grundy, Frank J.; Henkin, Tina M.

2015-01-01

The T box riboswitch regulates many amino acid-related genes in Gram-positive bacteria. T box riboswitch-mediated gene regulation was shown previously to occur at the level of transcription attenuation via structural rearrangements in the 5′ untranslated (leader) region of the mRNA in response to binding of a specific uncharged tRNA. In this study, a novel group of isoleucyl-tRNA synthetase gene (ileS) T box leader sequences found in organisms of the phylum Actinobacteria was investigated. The Stem I domains of these RNAs lack several highly conserved elements that are essential for interaction with the tRNA ligand in other T box RNAs. Many of these RNAs were predicted to regulate gene expression at the level of translation initiation through tRNA-dependent stabilization of a helix that sequesters a sequence complementary to the Shine–Dalgarno (SD) sequence, thus freeing the SD sequence for ribosome binding and translation initiation. We demonstrated specific binding to the cognate tRNAIle and tRNAIle-dependent structural rearrangements consistent with regulation at the level of translation initiation, providing the first biochemical demonstration, to our knowledge, of translational regulation in a T box riboswitch. PMID:25583497

Endophytic actinobacteria: Diversity, secondary metabolism and mechanisms to unsilence biosynthetic gene clusters.

PubMed

Dinesh, Raghavan; Srinivasan, Veeraraghavan; T E, Sheeja; Anandaraj, Muthuswamy; Srambikkal, Hamza

2017-09-01

Endophytic actinobacteria, which reside in the inner tissues of host plants, are gaining serious attention due to their capacity to produce a plethora of secondary metabolites (e.g. antibiotics) possessing a wide variety of biological activity with diverse functions. This review encompasses the recent reports on endophytic actinobacterial species diversity, in planta habitats and mechanisms underlying their mode of entry into plants. Besides, their metabolic potential, novel bioactive compounds they produce and mechanisms to unravel their hidden metabolic repertoire by activation of cryptic or silent biosynthetic gene clusters (BGCs) for eliciting novel secondary metabolite production are discussed. The study also reviews the classical conservative techniques (chemical/biological/physical elicitation, co-culturing) as well as modern microbiology tools (e.g. next generation sequencing) that are being gainfully employed to uncover the vast hidden scaffolds for novel secondary metabolites produced by these endophytes, which would subsequently herald a revolution in drug engineering. The potential role of these endophytes in the agro-environment as promising biological candidates for inhibition of phytopathogens and the way forward to thoroughly exploit this unique microbial community by inducing expression of cryptic BGCs for encoding unseen products with novel therapeutic properties are also discussed.

Structure, mineralogy, and microbial diversity of geothermal spring microbialites associated with a deep oil drilling in Romania.

PubMed

Coman, Cristian; Chiriac, Cecilia M; Robeson, Michael S; Ionescu, Corina; Dragos, Nicolae; Barbu-Tudoran, Lucian; Andrei, Adrian-Ştefan; Banciu, Horia L; Sicora, Cosmin; Podar, Mircea

2015-01-01

Modern mineral deposits play an important role in evolutionary studies by providing clues to the formation of ancient lithified microbial communities. Here we report the presence of microbialite-forming microbial mats in different microenvironments at 32°C, 49°C, and 65°C around the geothermal spring from an abandoned oil drill in Ciocaia, Romania. The mineralogy and the macro- and microstructure of the microbialites were investigated, together with their microbial diversity based on a 16S rRNA gene amplicon sequencing approach. The calcium carbonate is deposited mainly in the form of calcite. At 32°C and 49°C, the microbialites show a laminated structure with visible microbial mat-carbonate crystal interactions. At 65°C, the mineral deposit is clotted, without obvious organic residues. Partial 16S rRNA gene amplicon sequencing showed that the relative abundance of the phylum Archaea was low at 32°C (<0.5%) but increased significantly at 65°C (36%). The bacterial diversity was either similar to other microbialites described in literature (the 32°C sample) or displayed a specific combination of phyla and classes (the 49°C and 65°C samples). Bacterial taxa were distributed among 39 phyla, out of which 14 had inferred abundances >1%. The dominant bacterial groups at 32°C were Cyanobacteria, Gammaproteobacteria, Firmicutes, Bacteroidetes, Chloroflexi, Thermi, Actinobacteria, Planctomycetes, and Defferibacteres. At 49°C, there was a striking dominance of the Gammaproteobacteria, followed by Firmicutes, Bacteroidetes, and Armantimonadetes. The 65°C sample was dominated by Betaproteobacteria, Firmicutes, [OP1], Defferibacteres, Thermi, Thermotogae, [EM3], and Nitrospirae. Several groups from Proteobacteria and Firmicutes, together with Halobacteria and Melainabacteria were described for the first time in calcium carbonate deposits. Overall, the spring from Ciocaia emerges as a valuable site to probe microbes-minerals interrelationships along thermal and

Bloom of Firmicutes of order Bacillales underlies wet-up response of a cyanobacterial biocrust chronosequence

NASA Astrophysics Data System (ADS)

Karaoz, U.; Couradeau, E.; da Rocha, U. N.; Chien Lim, H.; Garcia-Pichel, F.; Northen, T.; Brodie, E.

2016-12-01

Biological soil crusts (biocrusts), critical components of dryland ecosystem, successionally develop to deliver a suite of ecosystem services. Biocrust assemblages are extremely well adapted to survive desiccation and then take advantage of pulses of precipitation typical of arid climate, yet we know little about how these microbial communities of different developmental stages respond to wetup. Here we focus on the wetup response of incipient cyanobacterial crusts as they progress from "light" to "dark". We sampled a cyanobacterial biocrust chronosequence pre- (dry) and post-wetup within a day, and used high-throughput 16S rRNA sequencing to decipher wetup response of microbial communities. Overall, changes in phylogenetic beta-diversity attributable to crust successional stage were at least as large as those for wetup. Notably, more mature crusts showed significantly higher resistance to pulse hydration. Taxonomically, a drastic bloom of handful Firmicutes taxa, primarily from Bacillales order was apparent 18 hrs. after wetup. The wetup response of filamentous cyanobacteria was variable across the successional gradient, with populations collapsing in less developed light crusts but rising in dark crusts. Strong phylogenetic clustering that significantly increased with crust development and wetup suggested conservation and an evolutionary basis for the response of biocrust microbial communities to wetup. The consistent Bacillales bloom accompanied by the variable collapse of the Microcoleus we documented across the successional gradient suggests that the cumulative effects of increased precipitation frequencies on C cycling will depend on crust maturity.

Deep 16S rRNA Pyrosequencing Reveals a Bacterial Community Associated with Banana Fusarium Wilt Disease Suppression Induced by Bio-Organic Fertilizer Application

PubMed Central

Ruan, Yunze; Xue, Chao; Zhang, Jian; Li, Rong; Shen, Qirong

2014-01-01

Our previous work demonstrated that application of a bio-organic fertilizer (BIO) to a banana mono-culture orchard with serious Fusarium wilt disease effectively decreased the number of soil Fusarium sp. and controlled the soil-borne disease. Because bacteria are an abundant and diverse group of soil organisms that responds to soil health, deep 16 S rRNA pyrosequencing was employed to characterize the composition of the bacterial community to investigate how it responded to BIO or the application of other common composts and to explore the potential correlation between bacterial community, BIO application and Fusarium wilt disease suppression. After basal quality control, 137,646 sequences and 9,388 operational taxonomic units (OTUs) were obtained from the 15 soil samples. Proteobacteria, Acidobacteria, Bacteroidetes, Gemmatimonadetes and Actinobacteria were the most frequent phyla and comprised up to 75.3% of the total sequences. Compared to the other soil samples, BIO-treated soil revealed higher abundances of Gemmatimonadetes and Acidobacteria, while Bacteroidetes were found in lower abundance. Meanwhile, on genus level, higher abundances compared to other treatments were observed for Gemmatimonas and Gp4. Correlation and redundancy analysis showed that the abundance of Gemmatimonas and Sphingomonas and the soil total nitrogen and ammonium nitrogen content were higher after BIO application, and they were all positively correlated with disease suppression. Cumulatively, the reduced Fusarium wilt disease incidence that was seen after BIO was applied for 1-year might be attributed to the general suppression based on a shift within the bacteria soil community, including specific enrichment of Gemmatimonas and Sphingomonas. PMID:24871319

Long-term forest soil warming alters microbial communities in temperate forest soils

PubMed Central

DeAngelis, Kristen M.; Pold, Grace; Topçuoğlu, Begüm D.; van Diepen, Linda T. A.; Varney, Rebecca M.; Blanchard, Jeffrey L.; Melillo, Jerry; Frey, Serita D.

2015-01-01

Soil microbes are major drivers of soil carbon cycling, yet we lack an understanding of how climate warming will affect microbial communities. Three ongoing field studies at the Harvard Forest Long-term Ecological Research (LTER) site (Petersham, MA) have warmed soils 5°C above ambient temperatures for 5, 8, and 20 years. We used this chronosequence to test the hypothesis that soil microbial communities have changed in response to chronic warming. Bacterial community composition was studied using Illumina sequencing of the 16S ribosomal RNA gene, and bacterial and fungal abundance were assessed using quantitative PCR. Only the 20-year warmed site exhibited significant change in bacterial community structure in the organic soil horizon, with no significant changes in the mineral soil. The dominant taxa, abundant at 0.1% or greater, represented 0.3% of the richness but nearly 50% of the observations (sequences). Individual members of the Actinobacteria, Alphaproteobacteria and Acidobacteria showed strong warming responses, with one Actinomycete decreasing from 4.5 to 1% relative abundance with warming. Ribosomal RNA copy number can obfuscate community profiles, but is also correlated with maximum growth rate or trophic strategy among bacteria. Ribosomal RNA copy number correction did not affect community profiles, but rRNA copy number was significantly decreased in warming plots compared to controls. Increased bacterial evenness, shifting beta diversity, decreased fungal abundance and increased abundance of bacteria with low rRNA operon copy number, including Alphaproteobacteria and Acidobacteria, together suggest that more or alternative niche space is being created over the course of long-term warming. PMID:25762989

Effect of long-term different fertilization on bacterial community structures and diversity in citrus orchard soil of volcanic ash.

PubMed

Joa, Jae Ho; Weon, Hang Yeon; Hyun, Hae Nam; Jeun, Young Chull; Koh, Sang Wook

2014-12-01

This study was conducted to assess bacterial species richness, diversity and community distribution according to different fertilization regimes for 16 years in citrus orchard soil of volcanic ash. Soil samples were collected and analyzed from Compost (cattle manure, 2,000 kg/10a), 1/2 NPK+compost (14-20-14+2,000 kg/10a), NPK+compost (28-40-28+2,000 kg/10a), NPK (28-40-28 kg/10a), 3 NPK (84-120-84 kg/10a), and Control (no fertilization) plot which have been managed in the same manners with compost and different amount of chemical fertilization. The range of pyrosequencing reads and OTUs were 4,687-7,330 and 1,790-3,695, respectively. Species richness estimates such as Ace, Chao1, and Shannon index were higher in 1/2 NPK+compost than other treatments, which were 15,202, 9,112, 7.7, respectively. Dominant bacterial groups at level of phylum were Proteobacteria, Acidobacteria, and Actinobacteria. Those were occupied at 70.9% in 1/2 NPK+compost. Dominant bacterial groups at level of genus were Pseudolabrys, Bradyrhizobium, and Acidobacteria. Those were distributed at 14.4% of a total of bacteria in Compost. Soil pH displayed significantly closely related to bacterial species richness estimates such as Ace, Chao1 (p<0.05) and Shannon index (p<0.01). However, it showed the negative correlation with exchangeable aluminum contents (p<0.05). In conclusion, diversity of bacterial community in citrus orchard soil was affected by fertilization management, soil pH changes and characteristics of volcanic ash.

Soil bacterial community response to vegetation succession after fencing in the grassland of China.

PubMed

Zeng, Quanchao; An, Shaoshan; Liu, Yang

2017-12-31

Natural succession is an important process in terrestrial system, playing an important role in enhancing soil quality and plant diversity. Soil bacteria is the linkage between soil and plant, has an important role in aboveground community dynamics and ecosystem functioning in terrestrial ecosystems, driving the decomposition of soil organic matter and plant litter. However, the role of soil bacteria in the secondary succession has not been well understood, particularly in the degraded soil of Loess Plateau. In this study, we investigated soil nutrients and soil bacterial community during the secondary succession after a long-term fencing in the grassland, in the Yuwu Mountain, northwest China. The chronosequence included 1year, 12years, 20years and 30years. The soil bacterial community composition was determined by the Illumina HiSeq sequencing method. The data showed that soil bacterial diversity had no significant changes along the chronosequence, but soil bacterial community compositions significantly changed. Proteobacteria, Acidobacteria and Actinobacteria were the main phyla in all the samples across succession. With the accumulation of soil organic matter and nutrients, the relative abundance of Actinobacteria decreased, whereas Proteobacteria increased. These shifts may be caused by the increase of the available nutrients across the secondary succession. In the younger sites, soils were dominated by oligotrophic groups, whereas soil in the late-succession site were dominated by copiotrophic groups, indicating the dependence of soil bacterial community composition on the contents of soil available nutrients. Copyright © 2017 Elsevier B.V. All rights reserved.

Bacterial diversity of Taxus rhizosphere: culture-independent and culture-dependent approaches.

PubMed

Hao, Da Cheng; Ge, Guang Bo; Yang, Ling

2008-07-01

The regional variability of Taxus rhizosphere bacterial community composition and diversity was studied by comparative analysis of three large 16S rRNA gene clone libraries from the Taxus rhizosphere in different regions of China (subtropical and temperate regions). One hundred and forty-six clones were screened for three libraries. Phylogenetic analysis of 16S rRNA gene sequences demonstrated that the abundance of sequences affiliated with Gammaproteobacteria, Betaproteobacteria, and Actinobacteria was higher in the library from the T. xmedia rhizosphere of the temperate region compared with the subtropical Taxus mairei rhizosphere. On the other hand, Acidobacteria was more abundant in libraries from the subtropical Taxus mairei rhizosphere. Richness estimates and diversity indices of three libraries revealed major differences, indicating a higher richness in the Taxus rhizosphere bacterial communities of the subtropical region and considerable variability in the bacterial community composition within this region. By enrichment culture, a novel Actinobacteria strain DICP16 was isolated from the T. xmedia rhizosphere of the temperate region and was identified as Leifsonia shinshuensis sp. via 16S rRNA gene and gyrase B sequence analyses. DICP16 was able to remove the xylosyl group from 7-xylosyl-10-deacetylbaccatin III and 7-xylosyl-10-deacetylpaclitaxel, thereby making the xylosyltaxanes available as sources of 10-deacetylbaccatin III and the anticancer drug paclitaxel. Taken together, the present studies provide, for the first time, the knowledge of the biodiversity of microorganisms populating Taxus rhizospheres.

[Phylogenetic diversity of microorganisms associated with the deep-water sponge Baikalospongia intermedia].

PubMed

Kalyzhnaya, O V; Itskovich, V B

2014-07-01

The diversity of bacteria associated with deep-water sponge Baikalospongia intermedia was evaluated by sequence analysis of 16S rRNA genes from two sponge samples collected in Lake Baikal from depths of 550 and 1204 m. A total of 64 operational taxonomic units, belonging to nine bacterial phyla, Proteobacteria (classes Alphaproteobacteria,. Betaproteobacteria, Gammaproteobacteria, and Deltaproteobacteria), Actinobacteria, Planctomycetes, Cloroflexi, Verrucomicrobia, Acidobacteria, Chlorobi, and Nitrospirae, including candidate phylum WS5, were identified. Phylogenetic analysis showed that the examined communities contained phylotypes exhibiting homology to uncultured bacteria from different lake ecosystems, freshwater sediments, soil and geological formations. Moreover, a number of phylotypes were relative to psychrophilic, methane-oxidizing, sulfate-reducing bacteria, and to microorganisms resistant to the influence of heavy metals. It seems likely that the unusual habitation conditions of deep-water sponges contribute to the taxonomic diversity of associated bacteria and have an influence on the presence of functionally important microorganisms in bacterial communities.

Soil microbial communities of three grassland ecosystems in the Bayinbuluke, China.

PubMed

Shao, Keqiang; Gao, Guang

2018-03-01

The microbial community plays an important role in soil nutrient cycles and energy transformations in alpine grassland. In this study, we investigated the composition of the soil microbial community collected from alpine cold swamp meadow (ASM), alpine cold meadow (AM), and alpine cold desert steppe (ADS) within the Bayinbuluke alpine grassland, China, using Illumina amplicon sequencing. Of the 147 271 sequences obtained, 36 microbial phyla or groups were detected. The results showed that the ADS had lower microbial diversity than the ASM and AM, as estimated by the Shannon index. The Verrucomicrobia, Chloroflexi, Planctomycetes, Proteobacteria, and Actinobacteria were the predominant phyla in all 3 ecosystems. Particularly, Thaumarchaeota was only abundant in ASM, Bacteroidetes in AM, and Acidobacteria in ADS. Additionally, the predominant genus also differed with each ecosystem. Candidatus Nitrososphaera was predominant in ADS, the Pir4 lineage in ASM, and Sphingomonas in AM. Our results indicated that the soil microbial community structure was different for each grassland ecosystem in the Bayinbuluke.

Genomic and Physiological Characterization of the Chromate-Reducing, Aquifer-Derived Firmicute Pelosinus sp. Strain HCF1

PubMed Central

Han, Ruyang; Karaoz, Ulas; Lim, HsiaoChien; Brodie, Eoin L.

2013-01-01

Pelosinus spp. are fermentative firmicutes that were recently reported to be prominent members of microbial communities at contaminated subsurface sites in multiple locations. Here we report metabolic characteristics and their putative genetic basis in Pelosinus sp. strain HCF1, an isolate that predominated anaerobic, Cr(VI)-reducing columns constructed with aquifer sediment. Strain HCF1 ferments lactate to propionate and acetate (the methylmalonyl-coenzyme A [CoA] pathway was identified in the genome), and its genome encodes two [NiFe]- and four [FeFe]-hydrogenases for H2 cycling. The reduction of Cr(VI) and Fe(III) may be catalyzed by a flavoprotein with 42 to 51% sequence identity to both ChrR and FerB. This bacterium has unexpected capabilities and gene content associated with reduction of nitrogen oxides, including dissimilatory reduction of nitrate to ammonium (two copies of NrfH and NrfA were identified along with NarGHI) and a nitric oxide reductase (NorCB). In this strain, either H2 or lactate can act as a sole electron donor for nitrate, Cr(VI), and Fe(III) reduction. Transcriptional studies demonstrated differential expression of hydrogenases and nitrate and nitrite reductases. Overall, the unexpected metabolic capabilities and gene content reported here broaden our perspective on what biogeochemical and ecological roles this species might play as a prominent member of microbial communities in subsurface environments. PMID:23064329

Microbial succession in an inflated lunar/Mars analog habitat during a 30-day human occupation.

PubMed

Mayer, Teresa; Blachowicz, Adriana; Probst, Alexander J; Vaishampayan, Parag; Checinska, Aleksandra; Swarmer, Tiffany; de Leon, Pablo; Venkateswaran, Kasthuri

2016-06-02

For potential future human missions to the Moon or Mars and sustained presence in the International Space Station, a safe enclosed habitat environment for astronauts is required. Potential microbial contamination of closed habitats presents a risk for crewmembers due to reduced human immune response during long-term confinement. To make future habitat designs safer for crewmembers, lessons learned from characterizing analogous habitats is very critical. One of the key issues is that how human presence influences the accumulation of microorganisms in the closed habitat. Molecular technologies, along with traditional microbiological methods, were utilized to catalog microbial succession during a 30-day human occupation of a simulated inflatable lunar/Mars habitat. Surface samples were collected at different time points to capture the complete spectrum of viable and potential opportunistic pathogenic bacterial population. Traditional cultivation, propidium monoazide (PMA)-quantitative polymerase chain reaction (qPCR), and adenosine triphosphate (ATP) assays were employed to estimate the cultivable, viable, and metabolically active microbial population, respectively. Next-generation sequencing was used to elucidate the microbial dynamics and community profiles at different locations of the habitat during varying time points. Statistical analyses confirm that occupation time has a strong influence on bacterial community profiles. The Day 0 samples (before human occupation) have a very different microbial diversity compared to the later three time points. Members of Proteobacteria (esp. Oxalobacteraceae and Caulobacteraceae) and Firmicutes (esp. Bacillaceae) were most abundant before human occupation (Day 0), while other members of Firmicutes (Clostridiales) and Actinobacteria (esp. Corynebacteriaceae) were abundant during the 30-day occupation. Treatment of samples with PMA (a DNA-intercalating dye for selective detection of viable microbial population) had a

Differences between bacterial communities in the gut of a soil-feeding termite (Cubitermes niokoloensis) and its mounds.

PubMed

Fall, Saliou; Hamelin, Jérôme; Ndiaye, Farma; Assigbetse, Komi; Aragno, Michel; Chotte, Jean Luc; Brauman, Alain

2007-08-01

In tropical ecosystems, termite mound soils constitute an important soil compartment covering around 10% of African soils. Previous studies have shown (S. Fall, S. Nazaret, J. L. Chotte, and A. Brauman, Microb. Ecol. 28:191-199, 2004) that the bacterial genetic structure of the mounds of soil-feeding termites (Cubitermes niokoloensis) is different from that of their surrounding soil. The aim of this study was to characterize the specificity of bacterial communities within mounds with respect to the digestive and soil origins of the mound. We have compared the bacterial community structures of a termite mound, termite gut sections, and surrounding soil using PCR-denaturing gradient gel electrophoresis (DGGE) analysis and cloning and sequencing of PCR-amplified 16S rRNA gene fragments. DGGE analysis revealed a drastic difference between the genetic structures of the bacterial communities of the termite gut and the mound. Analysis of 266 clones, including 54 from excised bands, revealed a high level of diversity in each biota investigated. The soil-feeding termite mound was dominated by the Actinobacteria phylum, whereas the Firmicutes and Proteobacteria phyla dominate the gut sections of termites and the surrounding soil, respectively. Phylogenetic analyses revealed a distinct clustering of Actinobacteria phylotypes between the mound and the surrounding soil. The Actinobacteria clones of the termite mound were diverse, distributed among 10 distinct families, and like those in the termite gut environment lightly dominated by the Nocardioidaceae family. Our findings confirmed that the soil-feeding termite mound (C. niokoloensis) represents a specific bacterial habitat in the tropics.

Culturable heterotrophic bacteria from the marine sponge Dendrilla nigra: isolation and phylogenetic diversity of actinobacteria

NASA Astrophysics Data System (ADS)

Selvin, Joseph; Gandhimathi, R.; Kiran, G. Seghal; Priya, S. Shanmugha; Ravji, T. Rajeetha; Hema, T. A.

2009-09-01

Culturable heterotrophic bacterial composition of marine sponge Dendrilla nigra was analysed using different enrichments. Five media compositions including without enrichment (control), enriched with sponge extract, with growth regulator (antibiotics), with autoinducers, and complete enrichment containing sponge extract, antibiotics, and autoinducers were developed. DNA hybridization assay was performed to explore host specific bacteria and ecotypes of culturable sponge-associated bacteria. Enrichment with selective inducers (AHLs and sponge extract) and regulators (antibiotics) considerably enhanced the cultivation potential of sponge-associated bacteria. It was found that Marinobacter (MSI032), Micromonospora (MSI033), Streptomyces (MSI051), and Pseudomonas (MSI057) were sponge-associated obligate symbionts. The present findings envisaged that “ Micromonospora-Saccharomonospora-Streptomyces” group was the major culturable actinobacteria in the marine sponge D. nigra. The DNA hybridization assay was a reliable method for the analysis of culturable bacterial community in marine sponges. Based on the culturable community structure, the sponge-associated bacteria can be grouped (ecotypes) as general symbionts, specific symbionts, habitat flora, and antagonists.

Molecular analysis of microbial diversity in corrosion samples from energy transmission towers.

PubMed

Oliveira, Valéria M; Lopes-Oliveira, Patrícia F; Passarini, Michel R Z; Menezes, Claudia B A; Oliveira, Walter R C; Rocha, Adriano J; Sette, Lara D

2011-04-01

Microbial diversity in corrosion samples from energy transmission towers was investigated using molecular methods. Ribosomal DNA fragments were used to assemble gene libraries. Sequence analysis indicated 10 bacterial genera within the phyla Proteobacteria, Firmicutes, Actinobacteria and Bacteroidetes. In the two libraries generated from corroded screw-derived samples, the genus Acinetobacter was the most abundant. Acinetobacter and Clostridium spp. dominated, with similar percentages, in the libraries derived from corrosion scrapings. Fungal clones were affiliated with 14 genera belonging to the phyla Ascomycota and Basidiomycota; of these, Capnobotryella and Fellomyces were the most abundant fungi observed. Several of the microorganisms had not previously been associated with biofilms and corrosion, reinforcing the need to use molecular techniques to achieve a more comprehensive assessment of microbial diversity in environmental samples.

Composition and variation of sediment bacterial and nirS-harboring bacterial communities at representative sites of the Bohai Gulf coastal zone, China.

PubMed

Guan, Xiangyu; Zhu, Lingling; Li, Youxun; Xie, Yuxuan; Zhao, Mingzhang; Luo, Ximing

2014-04-01

With rapid urbanization, anthropogenic activities are increasingly influencing the natural environment of the Bohai Bay. In this study, the composition and variation of bacterial and nirS-harboring bacterial communities in the coastal zone sediments of the Bohai Gulf were analyzed using PCR-based clone libraries. A total of 95 genera were detected in the bacterial communities, with Proteobacteria (72.1 %), Acidobacteria (10.5 %), Firmicutes (1.7 %), Bacteroidetes (1.4 %), Chloroflexi (0.7 %) and Planctomycetes (0.7 %) being the dominated phyla. The NirS sequences were divided into nine Clusters (A-I). Canonical correlation analysis showed that the bacterial or denitrifying communities were correlated with different environmental factors, such as total organic carbon, total nitrogen, ammonium, sulfate, etc. Furthermore, bacterial communities' composition and diversity are influenced by oil exploration, sewage discharge and other anthropogenic activities in the coastal area of the Bohai Sea. Thus, this study provided useful information on further research on regional or global environmental control and restore.

Effect of phenol on the nitrogen removal performance and microbial community structure and composition of an anammox reactor.

PubMed

Pereira, Alyne Duarte; Leal, Cíntia Dutra; Dias, Marcela França; Etchebehere, Claudia; Chernicharo, Carlos Augusto L; de Araújo, Juliana Calabria

2014-08-01

The effects of phenol on the nitrogen removal performance of a sequencing batch reactor (SBR) with anammox activity and on the microbial community within the reactor were evaluated. A phenol concentration of 300 mg L(-1) reduced the ammonium-nitrogen removal efficiency of the SBR from 96.5% to 47%. The addition of phenol changed the microbial community structure and composition considerably, as shown by denaturing gradient gel electrophoresis and 454 pyrosequencing of 16S rRNA genes. Some phyla, such as Proteobacteria, Verrucomicrobia, and Firmicutes, increased in abundance, whereas others, such as Acidobacteria, Chloroflexi, Planctomycetes, GN04, WS3, and NKB19, decreased. The diversity of the anammox bacteria was also affected by phenol: sequences related to Candidatus Brocadia fulgida were no longer detected, whereas sequences related to Ca. Brocadia sp. 40 and Ca. Jettenia asiatica persisted. These results indicate that phenol adversely affects anammox metabolism and changes the bacterial community within the anammox reactor. Copyright © 2014 Elsevier Ltd. All rights reserved.

Performance and bacterial community structure of a 10-years old constructed mangrove wetland.

PubMed

Tian, Tingting; Tam, Nora F Y; Zan, Qijie; Cheung, S G; Shin, Paul K S; Wong, Y S; Zhang, Li; Chen, Zhanghe

2017-11-30

Constructed mangrove wetland has been used for wastewater treatment but its long-term performance has not been reported. One-year monitoring of a 10-years old horizontal subsurface-flow constructed mangrove wetland consisting of three belts, two with mangrove plants and one without, revealed that the system maintained high and stable removal percentages of organic matter and nutrients, and planted belts performed better than unplanted control. Substrates in belts planted with Aegiceras corniculatum or Kandelia obovata had higher abundance of ammonifiers, nitrifiers and denitrifiers but lower total heterotrophic bacteria than unplanted substrate. Denaturing gradient gel electrophoresis showed that microbial diversity in planted substrate was significantly lower than that in unplanted one. The bacteria in substrates, irrespective to belts, were phylogenetically related to Proteobacteria (most dominant), Acidobacteria, Firmicutes, Nitrospirae, Gemmatimonadetes, Chloroflexi and Cyanobacteria. The steady performance of this 10-year old constructed mangrove wetland was affected by the abundance and diversity of bacterial community in substrate. Copyright © 2017 Elsevier Ltd. All rights reserved.

Quantification of Endospore-Forming Firmicutes by Quantitative PCR with the Functional Gene spo0A

PubMed Central

Bueche, Matthieu; Wunderlin, Tina; Roussel-Delif, Ludovic; Junier, Thomas; Sauvain, Loic; Jeanneret, Nicole

2013-01-01

Bacterial endospores are highly specialized cellular forms that allow endospore-forming Firmicutes (EFF) to tolerate harsh environmental conditions. EFF are considered ubiquitous in natural environments, in particular, those subjected to stress conditions. In addition to natural habitats, EFF are often the cause of contamination problems in anthropogenic environments, such as industrial production plants or hospitals. It is therefore desirable to assess their prevalence in environmental and industrial fields. To this end, a high-sensitivity detection method is still needed. The aim of this study was to develop and evaluate an approach based on quantitative PCR (qPCR). For this, the suitability of functional genes specific for and common to all EFF were evaluated. Seven genes were considered, but only spo0A was retained to identify conserved regions for qPCR primer design. An approach based on multivariate analysis was developed for primer design. Two primer sets were obtained and evaluated with 16 pure cultures, including representatives of the genera Bacillus, Paenibacillus, Brevibacillus, Geobacillus, Alicyclobacillus, Sulfobacillus, Clostridium, and Desulfotomaculum, as well as with environmental samples. The primer sets developed gave a reliable quantification when tested on laboratory strains, with the exception of Sulfobacillus and Desulfotomaculum. A test using sediment samples with a diverse EFF community also gave a reliable quantification compared to 16S rRNA gene pyrosequencing. A detection limit of about 104 cells (or spores) per gram of initial material was calculated, indicating this method has a promising potential for the detection of EFF over a wide range of applications. PMID:23811505

Microbially induced iron precipitation associated with a neutrophilic spring at Borra Caves, Vishakhapatnam, India.

PubMed

Baskar, Sushmitha; Baskar, Ramanathan; Thorseth, Ingunn H; Ovreås, Lise; Pedersen, Rolf B

2012-04-01

The present investigation uncovers various pieces of evidence for the possible biologically induced mineralization in iron mats associated with a pH-neutral spring in the Borra caves, Vishakhapatnam, India. Electron microscopy [scanning electron microscopy (SEM) and transmission electron microscopy (TEM)] demonstrated large numbers of (i) hollow tubes (diameter ∼1 μm) resembling sheaths of the iron-oxidizing bacteria Leptothrix, (ii) thin (diameter <1 μm) solid fibers of uncertain origin, (iii) nanoscale subspherical to irregularly shaped particles encrusting tubes and fibers, and (iv) aggregates of broken and partially disintegrated sheaths, fibers, and particles embedded in extracellular polymeric substances (EPS) occasionally including microbial cells. X-ray microanalyses by energy dispersive spectroscopy (EDS) revealed that the mat accumulated largely Fe but also smaller amounts of Si and traces of P and Ca. Particles rich in Si and Al (possibly kaolinite) and Ca (carbonate) were also observed. High-resolution TEM/EDS of unstained ultrathin sections suggests that microbial sheaths were highly mineralized by amorphous to cryptocrystalline Fe-rich phases and less frequently by other fine-grained and fibrous authigenic claylike minerals. Total number of microorganisms in the iron mats was 5.8×10(5) cells, g sed(-1) (wet weight). Analysis of the 16S rRNA gene diversity revealed microorganisms assigned to eight different phyla [Proteobacteria (62%), Chloroflexi (8%), Bacteroidetes (7%), Planctomycetes (1%), Actinobacteria (5%), Acidobacteria (6%), Nitrospira (1%), Firmicutes (5%)]. Within the Proteobacteria, Betaproteobacteria was the predominant class, which accounted for 28% of the sequences. Within this class some obvious similarities between the obtained sequences and sequences from other cave systems could be seen, especially sequences affiliated with Leptothrix, Siderooxidans, Crenothrix, Comamonadaceae, Dechloromonas, and many uncultured

Elucidation of rice rhizosphere metagenome in relation to methane and nitrogen metabolism under elevated carbon dioxide and temperature using whole genome metagenomic approach.

PubMed

Bhattacharyya, P; Roy, K S; Das, M; Ray, S; Balachandar, D; Karthikeyan, S; Nayak, A K; Mohapatra, T

2016-01-15

Carbon (C) and nitrogen (N) mineralization is one of the key processes of biogeochemical cycling in terrestrial ecosystem in general and rice ecology in particular. Rice rhizosphere is a rich niche of microbial diversity influenced by change in atmospheric temperature and concentration of carbon dioxide (CO2). Structural changes in microbial communities in rhizosphere influence the nutrient cycling. In the present study, the bacterial diversity and population dynamics were studied under ambient CO2 (a-CO2) and elevated CO2+temperature (e-CO2T) in lowland rice rhizosphere using whole genome metagenomic approach. The whole genome metagenomic sequence data of lowland rice exhibited the dominance of bacterial communities including Proteobacteria, Firmicutes, Acidobacteria, Actinobacteria and Planctomycetes. Interestingly, four genera related to methane production namely, Methanobacterium, Methanosphaera, Methanothermus and Methanothermococcus were absent in a-CO2 but noticed under e-CO2T. The acetoclastic pathway was found as the predominant pathway for methanogenesis, whereas, the serine pathway was found as the principal metabolic pathway for CH4 oxidation in lowland rice. The abundances of reads of enzymes in the acetoclastic methanogenesis pathway and serine pathways of methanotrophy were much higher in e-CO2T (328 and 182, respectively) as compared with a-CO2 (118 and 98, respectively). Rice rhizosphere showed higher structural diversities and functional activities in relation to N metabolism involving nitrogen fixation, assimilatory and dissimilatory nitrate reduction and denitrification under e-CO2T than that of a-CO2. Among the three pathways of N metabolism, dissimilarity pathways were predominant in lowland rice rhizosphere and more so under e-CO2T. Consequently, under e-CO2T, CH4 emission, microbial biomass nitrogen (MBN) and dehydrogenase activities were 45%, 20% and 35% higher than a-CO2, respectively. Holistically, a high bacterial diversity and

Multi-level comparisons of cloacal, skin, feather and nest-associated microbiota suggest considerable influence of horizontal acquisition on the microbiota assembly of sympatric woodlarks and skylarks.

PubMed

van Veelen, H Pieter J; Falcao Salles, Joana; Tieleman, B Irene

2017-12-01

Working toward a general framework to understand the role of microbiota in animal biology requires the characterisation of animal-associated microbial communities and identification of the evolutionary and ecological factors shaping their variation. In this study, we described the microbiota in the cloaca, brood patch skin and feathers of two species of birds and the microbial communities in their nest environment. We compared patterns of resemblance between these microbial communities at different levels of biological organisation (species, individual, body part) and investigated the phylogenetic structure to deduce potential microbial community assembly processes. Using 16S rRNA gene amplicon data of woodlarks (Lullula arborea) and skylarks (Alauda arvensis), we demonstrated that bird- and nest-associated microbiota showed substantial OTU co-occurrences and shared dominant taxonomic groups, despite variation in OTU richness, diversity and composition. Comparing host species, we uncovered that sympatric woodlarks and skylarks harboured similar microbiota, dominated by Proteobacteria, Firmicutes, Actinobacteria, Bacteroidetes and Acidobacteria. Yet, compared with the nest microbiota that showed little variation, each species' bird-associated microbiota displayed substantial variation. The latter could be partly (~ 20%) explained by significant inter-individual differences. The various communities of the bird's body (cloaca, brood patch skin and feathers) appeared connected with each other and with the nest microbiota (nest lining material and surface soil). Communities were more similar when the contact between niches was frequent or intense. Finally, bird microbiota showed significant phylogenetic clustering at the tips, but not at deeper branches of the phylogeny. Our interspecific comparison suggested that the environment is more important than phylogeny in shaping the bird-associated microbiotas. In addition, variation among individuals and among body parts

Cultivation-Based and Molecular Assessment of Bacterial Diversity in the Rhizosheath of Wheat under Different Crop Rotations

PubMed Central

Tahir, Muhammad; Mirza, M. Sajjad; Hameed, Sohail; Dimitrov, Mauricio R.; Smidt, Hauke

2015-01-01

A field study was conducted to compare the formationand bacterial communities of rhizosheaths of wheat grown under wheat-cotton and wheat-rice rotation and to study the effects of bacterial inoculation on plant growth. Inoculation of Azospirillum sp. WS-1 and Bacillus sp. T-34 to wheat plants increased root length, root and shoot dry weight and dry weight of rhizosheathsoil when compared to non-inoculated control plants, and under both crop rotations. Comparing both crop rotations, root length, root and shoot dry weight and dry weight of soil attached with roots were higher under wheat-cotton rotation. Organic acids (citric acid, malic acid, acetic acid and oxalic acid) were detected in rhizosheaths from both rotations, with malic acid being most abundant with 24.8±2 and 21.3±1.5 μg g-1 dry soil in wheat-cotton and wheat-rice rotation, respectively. Two sugars (sucrose, glucose) were detected in wheat rhizosheath under both rotations, with highest concentrations of sucrose (4.08±0.5 μg g-1and 7.36±1.0 μg g-1) and glucose (3.12±0.5 μg g-1 and 3.01± μg g-1) being detected in rhizosheaths of non-inoculated control plants under both rotations. Diversity of rhizosheath-associated bacteria was evaluated by cultivation, as well as by 454-pyrosequencing of PCR-tagged 16S rRNA gene amplicons. A total of 14 and 12 bacterial isolates predominantly belonging to the genera Arthrobacter, Azospirillum, Bacillus, Enterobacter and Pseudomonaswere obtained from the rhizosheath of wheat grown under wheat-cotton and wheat-rice rotation, respectively. Analysis of pyrosequencing data revealed Proteobacteria, Bacteriodetes and Verrucomicrobia as the most abundant phyla in wheat-rice rotation, whereas Actinobacteria, Firmicutes, Chloroflexi, Acidobacteria, Planctomycetes and Cyanobacteria were predominant in wheat-cotton rotation. From a total of 46,971 sequences, 10.9% showed ≥97% similarity with 16S rRNA genes of 32 genera previously shown to include isolates with plant

Successional trajectories of rhizosphere bacterial communities over consecutive seasons

DOE PAGES

Shi, Shengjing; Nuccio, Erin; Herman, Donald J.; ...

2015-08-04

It is well known that rhizosphere microbiomes differ from those of surrounding soil, and yet we know little about how these root-associated microbial communities change through the growing season and between seasons. We analyzed the response of soil bacteria to roots of the common annual grass Avena fatua over two growing seasons using high-throughput sequencing of 16S rRNA genes. Over the two periods of growth, the rhizosphere bacterial communities followed consistent successional patterns as plants grew, although the starting communities were distinct. Succession in the rhizosphere was characterized by a significant decrease in both taxonomic and phylogenetic diversity relative tomore » background soil communities, driven by reductions in both richness and evenness of the bacterial communities. Plant roots selectively stimulated the relative abundance of Alphaproteobacteria, Betaproteobacteria, and Bacteroidetes but reduced the abundance of Acidobacteria, Actinobacteria, and Firmicutes. Taxa that increased in relative abundance in the rhizosphere soil displayed phylogenetic clustering, suggesting some conservation and an evolutionary basis for the response of complex soil bacterial communities to the presence of plant roots. The reproducibility of rhizosphere succession and the apparent phylogenetic conservation of rhizosphere competence traits suggest adaptation of the indigenous bacterial community to this common grass over the many decades of its presence. We document the successional patterns of rhizosphere bacterial communities associated with a “wild” annual grass, Avena fatua, which is commonly a dominant plant in Mediterranean-type annual grasslands around the world; the plant was grown in its grassland soil. Most studies documenting rhizosphere microbiomes address “domesticated” plants growing in soils to which they are introduced. Rhizosphere bacterial communities exhibited a pattern of temporal succession that was consistent and repeatable

Successional trajectories of rhizosphere bacterial communities over consecutive seasons

DOE Office of Scientific and Technical Information (OSTI.GOV)

Shi, Shengjing; Nuccio, Erin; Herman, Donald J.

It is well known that rhizosphere microbiomes differ from those of surrounding soil, and yet we know little about how these root-associated microbial communities change through the growing season and between seasons. We analyzed the response of soil bacteria to roots of the common annual grass Avena fatua over two growing seasons using high-throughput sequencing of 16S rRNA genes. Over the two periods of growth, the rhizosphere bacterial communities followed consistent successional patterns as plants grew, although the starting communities were distinct. Succession in the rhizosphere was characterized by a significant decrease in both taxonomic and phylogenetic diversity relative tomore » background soil communities, driven by reductions in both richness and evenness of the bacterial communities. Plant roots selectively stimulated the relative abundance of Alphaproteobacteria, Betaproteobacteria, and Bacteroidetes but reduced the abundance of Acidobacteria, Actinobacteria, and Firmicutes. Taxa that increased in relative abundance in the rhizosphere soil displayed phylogenetic clustering, suggesting some conservation and an evolutionary basis for the response of complex soil bacterial communities to the presence of plant roots. The reproducibility of rhizosphere succession and the apparent phylogenetic conservation of rhizosphere competence traits suggest adaptation of the indigenous bacterial community to this common grass over the many decades of its presence. We document the successional patterns of rhizosphere bacterial communities associated with a “wild” annual grass, Avena fatua, which is commonly a dominant plant in Mediterranean-type annual grasslands around the world; the plant was grown in its grassland soil. Most studies documenting rhizosphere microbiomes address “domesticated” plants growing in soils to which they are introduced. Rhizosphere bacterial communities exhibited a pattern of temporal succession that was consistent and repeatable

Characterization of Endolithic Culturable Microbial Communities in Carbonate Rocks from a Typical Karst Canyon in Guizhou (China).

PubMed

Tang, Yuan; Cheng, Jian-Zhong; Lian, Bin

2017-01-02

The endolithic environment is a ubiquitous habitat for microorganisms and a critical interface between biology and geology. In this study, a culture-based method and the phylogenetic analysis based on 16S rRNA and internal transcribed spacer (ITS) sequences were used to investigate the diversity of endolithic bacteria and fungi in two main types of carbonate rocks (namely dolomite and limestone) from Nanjiang Canyon in Guizhou karst area, China. The results of bacterial diversity indicated that all bacteria isolated from dolomite and limestone rocks were divided into 4 bacterial groups, including Proteobacteria, Actinobacteria, Firmicutes and Bacteroidetes. For these two kinds of rocks, Proteobacteria was the first dominant group, and Gammaproteobacteria occupied the greatest proportion which might be closely related to Pseudomonas in phylogeny to be the most dominant genera after isolation. Actinobacteria and Bacillus bacteria were also widespread in these two kinds of rock environments. There were only 9 and 8 strains of fungi isolated from dolomite and limestone respectively, which all belonged to Ascomycota. To the best of our knowledge, this is the first report on diversity of endolithic culturable bacteria and fungi in carbonate rocks in Guizhou karst region. These microorganisms may play an important and unprecedented role in the carbonate rock weathering during the long history of geological evolution.

Microbial and viral-like rhodopsins present in coastal marine sediments from four polar and subpolar regions

DOE Office of Scientific and Technical Information (OSTI.GOV)

López, José L.; Golemba, Marcelo; Hernández, Edgardo

Rhodopsins are broadly distributed. In this work, we analyzed 23 metagenomes corresponding to marine sediment samples from four regions that share cold climate conditions (Norway; Sweden; Argentina and Antarctica). In order to investigate the genes evolution of viral rhodopsins, an initial set of 6224 bacterial rhodopsin sequences according to COG5524 were retrieved from the 23 metagenomes. After selection by the presence of transmembrane domains and alignment, 123 viral (51) and non-viral (72) sequences (>50 amino acids) were finally included in further analysis. Viral rhodopsin genes were homologs of Phaeocystis globosa virus and Organic lake Phycodnavirus. Non-viral microbial rhodopsin genes weremore » ascribed to Bacteroidetes, Planctomycetes, Firmicutes, Actinobacteria, Cyanobacteria, Proteobacteria, Deinococcus-Thermus and Cryptophyta and Fungi. A rescreening using Blastp, using as queries the viral sequences previously described, retrieved 30 sequences (>100 amino acids). Phylogeographic analysis revealed a geographical clustering of the sequences affiliated to the viral group. This clustering was not observed for the microbial non-viral sequences. The phylogenetic reconstruction allowed us to propose the existence of a putative ancestor of viral rhodopsin genes related to Actinobacteria and Chloroflexi. This is the first report about the existence of a phylogeographic association of the viral rhodopsin sequences from marine sediments.« less

Faecal microbiota in lean and obese dogs.

PubMed

Handl, Stefanie; German, Alexander J; Holden, Shelley L; Dowd, Scot E; Steiner, Jörg M; Heilmann, Romy M; Grant, Ryan W; Swanson, Kelly S; Suchodolski, Jan S

2013-05-01

Previous work has shown obesity to be associated with changes in intestinal microbiota. While obesity is common in dogs, limited information is available about the role of the intestinal microbiota. The aim of this study was to investigate whether alterations in the intestinal microbiota may be associated with canine obesity. Using 16S rRNA gene pyrosequencing and quantitative real-time PCR, we evaluated the composition of the faecal microbiota in 22 lean and 21 obese pet dogs, as well as in five research dogs fed ad libitum and four research dogs serving as lean controls. Firmicutes, Fusobacteria and Actinobacteria were the predominant bacterial phyla. The phylum Actinobacteria and the genus Roseburia were significantly more abundant in the obese pet dogs. The order Clostridiales significantly increased under ad libitum feeding in the research dogs. Canine intestinal microbiota is highly diverse and shows considerable interindividual variation. In the pet dogs, influence on the intestinal microbiota besides body condition, like age, breed, diet or lifestyle, might have masked the effect of obesity. The study population of research dogs was small, and further work is required before the role of the intestinal microbiota in canine obesity is clarified. © 2013 Federation of European Microbiological Societies. Published by Blackwell Publishing Ltd. All rights reserved.

Identities of epilithic hydrocarbon-utilizing diazotrophic bacteria from the Arabian Gulf Coasts, and their potential for oil bioremediation without nitrogen supplementation.

PubMed

Radwan, Samir; Mahmoud, Huda; Khanafer, Majida; Al-Habib, Aamar; Al-Hasan, Redha

2010-08-01

Gravel particles from four sites along the Arabian Gulf coast in autumn, winter, and spring were naturally colonized with microbial consortia containing between 7 and 400 × 10(2) cm(-2) of cultivable oil-utilizing bacteria. The 16S rRNA gene sequences of 70 representatives of oil-utilizing bacteria revealed that they were predominantly affiliated with the Gammaproteobacteria and the Actinobacteria. The Gammaproteobacteria comprised among others, the genera Pseudomonas, Pseudoalteromonas, Shewanella, Marinobacter, Psychrobacter, Idiomarina, Alcanivorax, Cobetia, and others. Actinobacteria comprised the genera Dietzia, Kocuria, Isoptericola, Rhodococcus, Microbacterium, and others. In autumn, Firmicutes members were isolated from bay and nonbay stations while Alphaproteobacteria were detected only during winter from Anjefa bay station. Fingerprinting by denaturing gradient gel electrophoresis of amplified 16S rRNA genes of whole microbial consortia confirmed the culture-based bacterial diversities in the various epilithons in various sites and seasons. Most of the representative oil-utilizing bacteria isolated from the epilithons were diazotrophic and could attenuate oil also in nitrogen-rich (7.9-62%) and nitrogen-free (4-54%) cultures, which, makes the microbial consortia suitable for oil bioremediation in situ, without need for nitrogen supplementation. This was confirmed in bench-scale experiments in which unfertilized oily seawater was bioremediated by epilithon-coated gravel particles.

Isolation and analysis of bacteria with antimicrobial activities from the marine sponge Haliclona simulans collected from Irish waters.

PubMed

Kennedy, Jonathan; Baker, Paul; Piper, Clare; Cotter, Paul D; Walsh, Marcella; Mooij, Marlies J; Bourke, Marie B; Rea, Mary C; O'Connor, Paula M; Ross, R Paul; Hill, Colin; O'Gara, Fergal; Marchesi, Julian R; Dobson, Alan D W

2009-01-01

Samples of the marine sponge Haliclona simulans were collected from Irish coastal waters, and bacteria were isolated from these samples. Phylogenetic analyses of the cultured isolates showed that four different bacterial phyla were represented; Bacteriodetes, Actinobacteria, Proteobacteria, and Firmicutes. The sponge bacterial isolates were assayed for the production of antimicrobial substances, and biological activities against Gram-positive and Gram-negative bacteria and fungi were demonstrated, with 50% of isolates showing antimicrobial activity against at least one of the test strains. Further testing showed that the antimicrobial activities extended to the important pathogens Pseudomonas aeruginosa, Clostridium difficile, multi-drug-resistant Staphylococcus aureus, and pathogenic yeast strains. The Actinomycetes were numerically the most abundant producers of antimicrobial activities, although activities were also noted from Bacilli and Pseudovibrio isolates. Surveys for the presence of potential antibiotic encoding polyketide synthase and nonribosomal peptide synthetase genes also revealed that genes for the biosynthesis of these secondary metabolites were present in most bacterial phyla but were particularly prevalent among the Actinobacteria and Proteobacteria. This study demonstrates that the culturable fraction of bacteria from the sponge H. simulans is diverse and appears to possess much potential as a source for the discovery of new medically relevant biological active agents.

Phylogenetic diversity and functional characterization of the Manila clam microbiota: a culture-based approach.

PubMed

Leite, Laura; Jude-Lemeilleur, Florence; Raymond, Natalie; Henriques, Isabel; Garabetian, Frédéric; Alves, Artur

2017-09-01

According to the hologenome theory, the microbiota contributes to the fitness of the holobiont having an important role in its adaptation, survival, development, health, and evolution. Environmental stress also affects the microbiota and its capability to assist the holobiont in coping with stress factors. Here, we analyzed the diversity of cultivable bacteria associated with Manila clam tissues (mantle, gills, hemolymph) in two non-contaminated sites (Portugal and France) and one metal-contaminated site (Portugal). A total of 240 isolates were obtained. Representative isolates (n = 198) of the overall diversity were identified by 16S rDNA sequencing and subjected to functional characterization. Isolates affiliated with Proteobacteria, Actinobacteria, Firmicutes, and Bacteroidetes. Proteobacteria (mostly Pseudoalteromonadaceae and Vibrionaceae) were dominant in non-contaminated sites while Actinobacteria (mostly Microbacteriaceae) dominated in the metal-contaminated site. The main factor affecting the microbiota composition was contamination. No significant differences were observed between clam tissues and geographic regions. Several isolates tested positive for antibacterial activity, biofilm formation, protease, and siderophore production. The results show that the Manila clam harbors a diverse microbiota that may contribute to clam protection and overall fitness, as well as to its adaptation to stressful environments. In addition, the Manila clam microbiota is revealed as a promising source of novel probiotics with potential application in aquaculture.

Culturable diversity of halophilic bacteria in foreshore soils

PubMed Central

Irshad, Aarzoo; Ahmad, Irshad; Kim, Seung Bum

2014-01-01

Halophilic bacteria are commonly found in natural environments containing significant concentration of NaCl such as inland salt lakes and evaporated sea-shore pools, as well as environments such as curing brines, salted food products and saline soils. Dependence on salt is an important phenotypic characteristic of halophilic bacteria, which can be used in the polyphasic characterization of newly discovered microorganisms. In this study the diversity of halophilic bacteria in foreshore soils of Daecheon, Chungnam, and Saemangeum, Jeonbuk, was investigated. Two types of media, namely NA and R2A supplemented with 3%, 5%, 9%, 15%, 20% and 30% NaCl were used. More than 200 halophilic bacteria were isolated and BOX-PCR fingerprinting analysis was done for the typing of the isolates. The BLAST identification results showed that isolated strains were composed of 4 phyla, Firmicutes (60%), Proteobacteria (31%), Bacteriodetes (5%) and Actinobacteria (4%). Isolates were affiliated with 16 genera and 36 species. Bacillus was the dominant genus in the phylum Firmicutes, comprising 24% of the total isolates. Halomonas (12%) and Shewanella (12%) were also found as the main genera. These findings show that the foreshore soil of Daecheon Beach and Saemangeum Sea of Korea represents an untapped source of bacterial biodiversity. PMID:25242943

Culturable diversity of halophilic bacteria in foreshore soils.

PubMed

Irshad, Aarzoo; Ahmad, Irshad; Kim, Seung Bum

2014-01-01

Halophilic bacteria are commonly found in natural environments containing significant concentration of NaCl such as inland salt lakes and evaporated sea-shore pools, as well as environments such as curing brines, salted food products and saline soils. Dependence on salt is an important phenotypic characteristic of halophilic bacteria, which can be used in the polyphasic characterization of newly discovered microorganisms. In this study the diversity of halophilic bacteria in foreshore soils of Daecheon, Chungnam, and Saemangeum, Jeonbuk, was investigated. Two types of media, namely NA and R2A supplemented with 3%, 5%, 9%, 15%, 20% and 30% NaCl were used. More than 200 halophilic bacteria were isolated and BOX-PCR fingerprinting analysis was done for the typing of the isolates. The BLAST identification results showed that isolated strains were composed of 4 phyla, Firmicutes (60%), Proteobacteria (31%), Bacteriodetes (5%) and Actinobacteria (4%). Isolates were affiliated with 16 genera and 36 species. Bacillus was the dominant genus in the phylum Firmicutes, comprising 24% of the total isolates. Halomonas (12%) and Shewanella (12%) were also found as the main genera. These findings show that the foreshore soil of Daecheon Beach and Saemangeum Sea of Korea represents an untapped source of bacterial biodiversity.

Composition and abundance of microbiota in the pharynx in patients with laryngeal carcinoma and vocal cord polyps.

PubMed

Gong, Hongli; Wang, Boyan; Shi, Yi; Shi, Yong; Xiao, Xiyan; Cao, Pengyu; Tao, Lei; Wang, Yuezhu; Zhou, Liang

2017-08-01

The pharynx is an important site of microbiota colonization, but the bacterial populations at this site have been relatively unexplored by culture-independent approaches. The aim of this study was to characterize the microbiota structure of the pharynx. Pyrosequencing of 16S rRNA gene libraries was used to characterize the pharyngeal microbiota using swab samples from 68 subjects with laryngeal cancer and 28 subjects with vocal cord polyps. Overall, the major phylum was Firmicutes, with Streptococcus as the predominant genus in the pharyngeal communities. Nine core operational taxonomic units detected from Streptococcus, Fusobacterium, Prevotella, Granulicatella, and Veillonella accounted for 21.3% of the total sequences detected. However, there was no difference in bacterial communities in the pharynx from patients with laryngeal cancer and vocal cord polyps. The relative abundance of Firmicutes was inversely correlated with Fusobacteria, Proteobacteria, Actinobacteria, and Bacteroidetes. The correlation was evident at the genus level, and the relative abundance of Streptococcus was inversely associated with Fusobacterium, Leptotrichia, Neisseria, Actinomyces, and Prevotella. This study presented a profile for the overall structure of the microbiota in pharyngeal swab samples. Inverse correlations were found between Streptococcus and other bacterial communities, suggesting that potential antagonism may exist among pharyngeal microbiota.

Characterisation of caecum and crop microbiota of Indian indigenous chicken targeting multiple hypervariable regions within 16S rRNA gene.

PubMed

Saxena, S; Saxena, V K; Tomar, S; Sapcota, D; Gonmei, G

2016-06-01

A comparative analysis of caecum and crop microbiota of chick, grower and adult stages of Indian indigenous chickens was conducted to investigate the role of the microbiota of the gastrointestinal tract, which play an important role in host performance, health and immunity. High-throughput Illumina sequencing was performed for V3, V4 and V4-V6 hypervariable regions of the 16S rRNA gene. M5RNA and M5NR databases under MG-RAST were used for metagenomic datasets annotation. In the crop, Firmicutes (~78%) and Proteobacteria (~16%) were the predominant phyla whereas in the caecum, Firmicutes (~50%), Bacteroidetes (~29%) and Actinobacteria (~10%) were predominant. The Shannon-Wiener diversity index suggested that sample richness and diversity increased as the chicken aged. For the first time, the presence of Lactobacillus species such as L. frumenti, L. antri, L. mucosae in the chicken crop along with Kineococcus radiotolerans, Desulfohalobium retbaense and L. jensenii in the caecum are reported. Many of these bacterial species have been found to be involved in immune response modulation and disease prevention in pigs and humans. The gut microbiome of the indigenous chicken was enriched with microbes having probiotic potential which might be essential for their adaptability.

Genome-wide gene order distances support clustering the gram-positive bacteria

PubMed Central

House, Christopher H.; Pellegrini, Matteo; Fitz-Gibbon, Sorel T.

2015-01-01

Initially using 143 genomes, we developed a method for calculating the pair-wise distance between prokaryotic genomes using a Monte Carlo method to estimate the conservation of gene order. The method was based on repeatedly selecting five or six non-adjacent random orthologs from each of two genomes and determining if the chosen orthologs were in the same order. The raw distances were then corrected for gene order convergence using an adaptation of the Jukes-Cantor model, as well as using the common distance correction D′ = −ln(1-D). First, we compared the distances found via the order of six orthologs to distances found based on ortholog gene content and small subunit rRNA sequences. The Jukes-Cantor gene order distances are reasonably well correlated with the divergence of rRNA (R2 = 0.24), especially at rRNA Jukes-Cantor distances of less than 0.2 (R2 = 0.52). Gene content is only weakly correlated with rRNA divergence (R2 = 0.04) over all distances, however, it is especially strongly correlated at rRNA Jukes-Cantor distances of less than 0.1 (R2 = 0.67). This initial work suggests that gene order may be useful in conjunction with other methods to help understand the relatedness of genomes. Using the gene order distances in 143 genomes, the relations of prokaryotes were studied using neighbor joining and agreement subtrees. We then repeated our study of the relations of prokaryotes using gene order in 172 complete genomes better representing a wider-diversity of prokaryotes. Consistently, our trees show the Actinobacteria as a sister group to the bulk of the Firmicutes. In fact, the robustness of gene order support was found to be considerably greater for uniting these two phyla than for uniting any of the proteobacterial classes together. The results are supportive of the idea that Actinobacteria and Firmicutes are closely related, which in turn implies a single origin for the gram-positive cell. PMID:25653643

The development of lower respiratory tract microbiome in mice.

PubMed

Singh, Nisha; Vats, Asheema; Sharma, Aditi; Arora, Amit; Kumar, Ashwani

2017-06-21

Although culture-independent methods have paved the way for characterization of the lung microbiome, the dynamic changes in the lung microbiome from neonatal stage to adult age have not been investigated. In this study, we tracked changes in composition and diversity of the lung microbiome in C57BL/6N mice, starting from 1-week-old neonates to 8-week-old mice. Towards this, the lungs were sterilely excised from mice of different ages from 1 to 8 weeks. High-throughput DNA sequencing of the 16S rRNA gene followed by composition and diversity analysis was utilized to decipher the microbiome in these samples. Microbiome analysis suggests that the changes in the lung microbiome correlated with age. The lung microbiome was primarily dominated by phyla Proteobacteria, Firmicutes, Bacteroidetes, and Actinobacteria in all the stages from week 1 to week 8 after birth. Although Defluvibacter was the predominant genus in 1-week-old neonatal mice, Streptococcus became the dominant genus at the age of 2 weeks. Lactobacillus, Defluvibacter, Streptococcus, and Achromobacter were the dominant genera in 3-week-old mice, while Lactobacillus and Achromobacter were the most abundant genera in 4-week-old mice. Interestingly, relatively greater diversity (at the genus level) during the age of 5 to 6 weeks was observed as compared to the earlier weeks. The diversity of the lung microbiome remained stable between 6 and 8 weeks of age. In summary, we have tracked the development of the lung microbiome in mice from an early age of 1 week to adulthood. The lung microbiome is dominated by the phyla Proteobacteria, Firmicutes, Bacteroidetes, and Actinobacteria. However, dynamic changes were observed at the genus level. Relatively higher richness in the microbial diversity was achieved by age of 6 weeks and then maintained at later ages. We believe that this study improves our understanding of the development of the mice lung microbiome and will facilitate further analyses of the role of

Genomic islands link secondary metabolism to functional adaptation in marine Actinobacteria

PubMed Central

Penn, Kevin; Jenkins, Caroline; Nett, Markus; Udwary, Daniel W.; Gontang, Erin A.; McGlinchey, Ryan P.; Foster, Brian; Lapidus, Alla; Podell, Sheila; Allen, Eric E.; Moore, Bradley S.; Jensen, Paul R.

2009-01-01

Genomic islands have been shown to harbor functional traits that differentiate ecologically distinct populations of environmental bacteria. A comparative analysis of the complete genome sequences of the marine Actinobacteria Salinispora tropica and S. arenicola reveals that 75% of the species-specific genes are located in 21 genomic islands. These islands are enriched in genes associated with secondary metabolite biosynthesis providing evidence that secondary metabolism is linked to functional adaptation. Secondary metabolism accounts for 8.8% and 10.9% of the genes in the S. tropica and S. arenicola genomes, respectively, and represents the major functional category of annotated genes that differentiates the two species. Genomic islands harbor all 25 of the species-specific biosynthetic pathways, the majority of which occur in S. arenicola and may contribute to the cosmopolitan distribution of this species. Genome evolution is dominated by gene duplication and acquisition, which in the case of secondary metabolism provide immediate opportunities for the production of new bioactive products. Evidence that secondary metabolic pathways are exchanged horizontally, coupled with prior evidence for fixation among globally distributed populations, supports a functional role and suggests that the acquisition of natural product biosynthetic gene clusters represents a previously unrecognized force driving bacterial diversification. Species-specific differences observed in CRISPR (clustered regularly interspaced short palindromic repeat) sequences suggest that S. arenicola may possess a higher level of phage immunity, while a highly duplicated family of polymorphic membrane proteins provides evidence of a new mechanism of marine adaptation in Gram-positive bacteria. PMID:19474814

Selective progressive response of soil microbial community to wild oat roots.

PubMed

DeAngelis, Kristen M; Brodie, Eoin L; DeSantis, Todd Z; Andersen, Gary L; Lindow, Steven E; Firestone, Mary K

2009-02-01

Roots moving through soil induce physical and chemical changes that differentiate rhizosphere from bulk soil, and the effects of these changes on soil microorganisms have long been a topic of interest. The use of a high-density 16S rRNA microarray (PhyloChip) for bacterial and archaeal community analysis has allowed definition of the populations that respond to the root within the complex grassland soil community; this research accompanies compositional changes reported earlier, including increases in chitinase- and protease-specific activity, cell numbers and quorum sensing signal. PhyloChip results showed a significant change compared with bulk soil in relative abundance for 7% of the total rhizosphere microbial community (147 of 1917 taxa); the 7% response value was confirmed by16S rRNA terminal restriction fragment length polymorphism analysis. This PhyloChip-defined dynamic subset was comprised of taxa in 17 of the 44 phyla detected in all soil samples. Expected rhizosphere-competent phyla, such as Proteobacteria and Firmicutes, were well represented, as were less-well-documented rhizosphere colonizers including Actinobacteria, Verrucomicrobia and Nitrospira. Richness of Bacteroidetes and Actinobacteria decreased in soil near the root tip compared with bulk soil, but then increased in older root zones. Quantitative PCR revealed rhizosphere abundance of beta-Proteobacteria and Actinobacteria at about 10(8) copies of 16S rRNA genes per g soil, with Nitrospira having about 10(5) copies per g soil. This report demonstrates that changes in a relatively small subset of the soil microbial community are sufficient to produce substantial changes in functions observed earlier in progressively more mature rhizosphere zones.

Analysis of bacterial and fungal communities in Marcha and Thiat, traditionally prepared amylolytic starters of India.

PubMed

Sha, Shankar Prasad; Jani, Kunal; Sharma, Avinash; Anupma, Anu; Pradhan, Pooja; Shouche, Yogesh; Tamang, Jyoti Prakash

2017-09-08

Marcha and thiat are traditionally prepared amylolytic starters use for production of various ethnic alcoholic beverages in Sikkim and Meghalaya states in India. In the present study we have tried to investigate the bacterial and fungal community composition of marcha and thiat by using high throughput sequencing. Characterization of bacterial community depicts phylum Proteobacteria is the most dominant in both marcha (91.4%) and thiat (53.8%), followed by Firmicutes, and Actinobacteria. Estimates of fungal community composition showed Ascomycota as the dominant phylum. Presence of Zygomycota in marcha distinguishes it from the thiat. The results of NGS analysis revealed dominance of yeasts in marcha whereas molds out numbers in case of thiat. This is the first report on microbial communities of traditionally prepared amylolytic starters of India using high throughput sequencing.

Integrated metagenomics and molecular ecological network analysis of bacterial community composition during the phytoremediation of cadmium-contaminated soils by bioenergy crops.

PubMed

Chen, Zhaojin; Zheng, Yuan; Ding, Chuanyu; Ren, Xuemin; Yuan, Jian; Sun, Feng; Li, Yuying

2017-11-01

Two energy crops (maize and soybean) were used in the remediation of cadmium-contaminated soils. These crops were used because they are fast growing, have a large biomass and are good sources for bioenergy production. The total accumulation of cadmium in maize and soybean plants was 393.01 and 263.24μg pot -1 , respectively. The rhizosphere bacterial community composition was studied by MiSeq sequencing. Phylogenetic analysis was performed using 16S rRNA gene sequences. The rhizosphere bacteria were divided into 33 major phylogenetic groups according to phyla. The dominant phylogenetic groups included Proteobacteria, Acidobacteria, Actinobacteria, Gemmatimonadetes, and Bacteroidetes. Based on principal component analysis (PCA) and unweighted pair group with arithmetic mean (UPGMA) analysis, we found that the bacterial community was influenced by cadmium addition and bioenergy cropping. Three molecular ecological networks were constructed for the unplanted, soybean- and maize-planted bacterial communities grown in 50mgkg -1 cadmium-contaminated soils. The results indicated that bioenergy cropping increased the complexity of the bacterial community network as evidenced by a higher total number of nodes, the average geodesic distance (GD), the modularity and a shorter geodesic distance. Proteobacteria and Acidobacteria were the keystone bacteria connecting different co-expressed operational taxonomic units (OTUs). The results showed that bioenergy cropping altered the topological roles of individual OTUs and keystone populations. This is the first study to reveal the effects of bioenergy cropping on microbial interactions in the phytoremediation of cadmium-contaminated soils by network reconstruction. This method can greatly enhance our understanding of the mechanisms of plant-microbe-metal interactions in metal-polluted ecosystems. Copyright © 2017 Elsevier Inc. All rights reserved.

Urbanization Reduces Transfer of Diverse Environmental Microbiota Indoors

PubMed Central

Parajuli, Anirudra; Grönroos, Mira; Siter, Nathan; Puhakka, Riikka; Vari, Heli K.; Roslund, Marja I.; Jumpponen, Ari; Nurminen, Noora; Laitinen, Olli H.; Hyöty, Heikki; Rajaniemi, Juho; Sinkkonen, Aki

2018-01-01

Expanding urbanization is a major factor behind rapidly declining biodiversity. It has been proposed that in urbanized societies, the rarity of contact with diverse environmental microbiota negatively impacts immune function and ultimately increases the risk for allergies and other immune-mediated disorders. Surprisingly, the basic assumption that urbanization reduces exposure to environmental microbiota and its transfer indoors has rarely been examined. We investigated if the land use type around Finnish homes affects the diversity, richness, and abundance of bacterial communities indoors. Debris deposited on standardized doormats was collected in 30 rural and 26 urban households in and near the city of Lahti, Finland, in August 2015. Debris was weighed, bacterial community composition determined by high throughput sequencing of bacterial 16S ribosomal RNA (rRNA) gene on the Illumina MiSeq platform, and the percentage of four different land use types (i.e., built area, forest, transitional, and open area) within 200 m and 2000 m radiuses from each household was characterized. The quantity of doormat debris was inversely correlated with coverage of built area. The diversity of total bacterial, Proteobacterial, Actinobacterial, Bacteroidetes, and Firmicutes communities decreased as the percentage of built area increased. Their richness followed the same pattern except for Firmicutes for which no association was observed. The relative abundance of Proteobacteria and particularly Gammaproteobacteria increased, whereas that of Actinobacteria decreased with increasing built area. Neither Phylum Firmicutes nor Bacteroidetes varied with coverage of built area. Additionally, the relative abundance of potentially pathogenic bacterial families and genera increased as the percentage of built area increased. Interestingly, having domestic animals (including pets) only altered the association between the richness of Gammaproteobacteria and diversity of Firmicutes with the built

Structure, mineralogy, and microbial diversity of geothermal spring microbialites associated with a deep oil drilling in Romania

PubMed Central

Coman, Cristian; Chiriac, Cecilia M.; Robeson, Michael S.; Ionescu, Corina; Dragos, Nicolae; Barbu-Tudoran, Lucian; Andrei, Adrian-Ştefan; Banciu, Horia L.; Sicora, Cosmin; Podar, Mircea

2015-01-01

Modern mineral deposits play an important role in evolutionary studies by providing clues to the formation of ancient lithified microbial communities. Here we report the presence of microbialite-forming microbial mats in different microenvironments at 32°C, 49°C, and 65°C around the geothermal spring from an abandoned oil drill in Ciocaia, Romania. The mineralogy and the macro- and microstructure of the microbialites were investigated, together with their microbial diversity based on a 16S rRNA gene amplicon sequencing approach. The calcium carbonate is deposited mainly in the form of calcite. At 32°C and 49°C, the microbialites show a laminated structure with visible microbial mat-carbonate crystal interactions. At 65°C, the mineral deposit is clotted, without obvious organic residues. Partial 16S rRNA gene amplicon sequencing showed that the relative abundance of the phylum Archaea was low at 32°C (<0.5%) but increased significantly at 65°C (36%). The bacterial diversity was either similar to other microbialites described in literature (the 32°C sample) or displayed a specific combination of phyla and classes (the 49°C and 65°C samples). Bacterial taxa were distributed among 39 phyla, out of which 14 had inferred abundances >1%. The dominant bacterial groups at 32°C were Cyanobacteria, Gammaproteobacteria, Firmicutes, Bacteroidetes, Chloroflexi, Thermi, Actinobacteria, Planctomycetes, and Defferibacteres. At 49°C, there was a striking dominance of the Gammaproteobacteria, followed by Firmicutes, Bacteroidetes, and Armantimonadetes. The 65°C sample was dominated by Betaproteobacteria, Firmicutes, [OP1], Defferibacteres, Thermi, Thermotogae, [EM3], and Nitrospirae. Several groups from Proteobacteria and Firmicutes, together with Halobacteria and Melainabacteria were described for the first time in calcium carbonate deposits. Overall, the spring from Ciocaia emerges as a valuable site to probe microbes-minerals interrelationships along thermal and

Structure, mineralogy, and microbial diversity of geothermal spring microbialites associated with a deep oil drilling in Romania

DOE PAGES

Coman, Cristian; Chiriac, Cecilia M.; Robeson, Michael S.; ...

2015-03-30

Modern mineral deposits play an important role in evolutionary studies by providing clues to the formation of ancient lithified microbial communities. Here we report the presence of microbialite-forming microbial mats in different microenvironments at 32°C, 49°C, and 65°C around the geothermal spring from an abandoned oil drill in Ciocaia, Romania. The mineralogy and the macro- and microstructure of the microbialites were investigated, together with their microbial diversity based on a 16S rRNA gene amplicon sequencing approach. The calcium carbonate is deposited mainly in the form of calcite. At 32°C and 49°C, the microbialites show a laminated structure with visible microbialmore » mat-carbonate crystal interactions. At 65°C, the mineral deposit is clotted, without obvious organic residues. Partial 16S rRNA gene amplicon sequencing showed that the relative abundance of the phylum Archaea was low at 32°C (<0.5%) but increased significantly at 65°C (36%). The bacterial diversity was either similar to other microbialites described in literature (the 32°C sample) or displayed a specific combination of phyla and classes (the 49°C and 65°C samples). Bacterial taxa were distributed among 39 phyla, out of which 14 had inferred abundances >1%. The dominant bacterial groups at 32°C were Cyanobacteria, Gammaproteobacteria, Firmicutes, Bacteroidetes, Chloroflexi, Thermi, Actinobacteria, Planctomycetes, and Defferibacteres. At 49°C, there was a striking dominance of the Gammaproteobacteria, followed by Firmicutes, Bacteroidetes, and Armantimonadetes. The 65°C sample was dominated by Betaproteobacteria, Firmicutes, [OP1], Defferibacteres, Thermi, Thermotogae, [EM3], and Nitrospirae. Lastly, several groups from Proteobacteria and Firmicutes, together with Halobacteria and Melainabacteria were described for the first time in calcium carbonate deposits. Overall, the spring from Ciocaia emerges as a valuable site to probe microbes-minerals interrelationships along

Association study of Demodex bacteria and facial dermatoses based on DGGE technique.

PubMed

Zhao, YaE; Yang, Fan; Wang, RuiLing; Niu, DongLing; Mu, Xin; Yang, Rui; Hu, Li

2017-03-01

The role of bacteria is unclear in the facial skin lesions caused by Demodex. To shed some light on this issue, we conducted a case-control study comparing cases with facial dermatoses with controls with healthy skin using denaturing gradient gel electrophoresis (DGGE) technique. The bacterial diversity, composition, and principal component were analyzed for Demodex bacteria and the matched facial skin bacteria. The result of mite examination showed that all 33 cases were infected with Demodex folliculorum (D. f), whereas 16 out of the 30 controls were infected with D. f, and the remaining 14 controls were infected with Demodex brevis (D. b). The diversity analysis showed that only evenness index presented statistical difference between mite bacteria and matched skin bacteria in the cases. The composition analysis showed that the DGGE bands of cases and controls were assigned to 12 taxa of 4 phyla, including Proteobacteria (39.37-52.78%), Firmicutes (2.7-26.77%), Actinobacteria (0-5.71%), and Bacteroidetes (0-2.08%). In cases, the proportion of Staphylococcus in Firmicutes was significantly higher than that in D. f controls and D. b controls, while the proportion of Sphingomonas in Proteobacteria was significantly lower than that in D. f controls. The between-group analysis (BGA) showed that all the banding patterns clustered into three groups, namely, D. f cases, D. f controls, and D. b controls. Our study suggests that the bacteria in Demodex should come from the matched facial skin bacteria. Proteobacteria and Firmicutes are the two main taxa. The increase of Staphylococcus and decrease of Sphingomonas might be associated with the development of facial dermatoses.

Actinobacteria Associated With Arbuscular Mycorrhizal Funneliformis mosseae Spores, Taxonomic Characterization and Their Beneficial Traits to Plants: Evidence Obtained From Mung Bean (Vigna radiata) and Thai Jasmine Rice (Oryza sativa)

PubMed Central

Lasudee, Krisana; Tokuyama, Shinji; Lumyong, Saisamorn; Pathom-aree, Wasu

2018-01-01

In this study, we report on the isolation of actinobacteria obtained from spores of Funneliformis mosseae and provide evidence for their potential in agricultural uses as plant growth promoters in vitro and in vivo. Actinobacteria were isolated from spores of F. mosseae using the dilution plate technique and media designed for the selective isolation of members of specific actinobacterial taxa. Six strains namely 48, S1, S3, S4, S4-1 and SP, were isolated and identified based on16S rRNA gene sequences. Phylogenetic analysis showed that isolate SP belonged to the genus Pseudonocardia with P. nantongensis KLBMP 1282T as its closest neighbor. The remaining isolates belonged to the genus Streptomyces. Two isolates, 48 and S3 were most closely related to S. thermocarboxydus DSM 44293T. Isolates S4 and S4-1 shared the highest 16S RNA gene similarity with S. pilosus NBRC 127772T. Isolate S1 showed its closest relationship with the type strain of S. spinoverrucosus NBRC14228T. The ability of these isolates to produce indole-3-acetic acid (IAA), siderophores and the ability to solubilize phosphate in vitro were examined. All isolates produced siderophores, four isolates produced IAA and two isolates solubilized inorganic phosphate at varying levels. S. thermocarboxydus isolate S3 showed the highest IAA production with high activities of phosphate solubilization and siderophore production. The inoculation of mung beans (Vigna radiata) with this strain resulted in a significant increase in fresh weight, root length and total length as an effect of IAA production. In an experiment with rice (Oryza sativa), S. thermocarboxydus isolate S3 promoted the growth of rice plants grown in low nutritional soil under induced drought stress. This report supports the view that the inoculation of rice with plant growth promoting actinobacteria mitigates some adverse effects of low nutrient and drought stress on rice. PMID:29942292

Atmospheric Deposition-Carried Zn and Cd from a Zinc Smelter and Their Effects on Soil Microflora as Revealed by 16S rDNA

PubMed Central

Shen, Feng; Li, Yanxia; Zhang, Min; Awasthi, Mukesh Kumar; Ali, Amjad; Li, Ronghua; Wang, Quan; Zhang, Zengqiang

2016-01-01

In this study, we investigated the influence of heavy metals (HM) on total soil bacterial population and its diversity pattern from 10 km distance of a Zinc smelter in Feng County, Qinling Mountain, China. We characterized and identified the bacterial community in a HM polluted soil using 16S rDNA technology. Out results indicated that the maximum soil HM concentration and the minimum bacterial population were observed in S2 soil, whereas bacterial diversity raised with the sampling distance increased. The bacterial communities were dominated by the phyla Proteobacteria, Acidobacteria and Actinobacteria in cornfield soils, except Fimicutes phylum which dominated in hilly area soil. The soil CEC, humic acid (HA)/fulvic acid (FA) and microbial OTUs increased with the sampling distance increased. Shewanella, Halomonas and Escherichia genera were highly tolerant to HM stress in both cultivated and non-cultivated soil. Finally, we found a consistent correlation of bacterial diversity with total HM and SOM along the sampling distance surrounding the zinc smelter, which could provide a new insight into the bacterial community-assisted and phytoremediation of HM contaminated soils. PMID:27958371

[Effects of intercropping Chinese onion cultivars of different allelopathic potential on cucumber growth and soil micro-environment].

PubMed

Yang, Yang; Wu, Feng-zhi

2011-10-01

A pot experiment was conducted to study the effects of intercropping various Chinese onion cultivars of different allelopathic potential on the cucumber growth and rhizospheric soil environment. When intercropped with high allelopathic Chinese onion cultivars, the EC value and peroxidase activity of cucumber rhizospheric soil decreased, while the pH value, invertase and catalase activities, and bacterial community diversity increased. The cloning and sequencing results indicated that most DGGE bands amplified from cucumber rhizospheric soil samples showed a high homology to uncultured bacterial species. The common bands were affiliated with Actinobacteria and Proteobacteria, and the differential bacteria bands were affiliated with Proteobacteria and Anaerolineaceae. Rhodospirillales and Acidobacteria were only found in the cucumber rhizospheric soil intercropped with low allelopathic Chinese onion cultivars. Correlation analysis showed that there were significant positive correlations between rhizospheric soil urease activity and cucumber seedlings height, total dry biomass, leaf area, and DGGE band number. It was suggested that intercropping high allelopathic Chinese onion cultivars could establish a good rhizospheric soil micro-environment for cucumber growth, and promote the growth of cucumber seedlings markedly.

Diversity of extremophilic bacteria in the sediment of high-altitude lakes located in the mountain desert of Ojos del Salado volcano, Dry-Andes.

PubMed

Aszalós, Júlia Margit; Krett, Gergely; Anda, Dóra; Márialigeti, Károly; Nagy, Balázs; Borsodi, Andrea K

2016-09-01

Ojos del Salado, the highest volcano on Earth is surrounded by a special mountain desert with extreme aridity, great daily temperature range, intense solar radiation, and permafrost from 5000 meters above sea level. Several saline lakes and permafrost derived high-altitude lakes can be found in this area, often surrounded by fumaroles and hot springs. The aim of this study was to gain information about the bacterial communities inhabiting the sediment of high-altitude lakes of the Ojos del Salado region located between 3770 and 6500 m. Altogether 11 sediment samples from 4 different altitudes were examined with 16S rRNA gene based denaturing gradient gel electrophoresis and clone libraries. Members of 17 phyla or candidate divisions were detected with the dominance of Proteobacteria, Acidobacteria, Actinobacteria and Bacteroidetes. The bacterial community composition was determined mainly by the altitude of the sampling sites; nevertheless, the extreme aridity and the active volcanism had a strong influence on it. Most of the sequences showed the highest relation to bacterial species or uncultured clones from similar extreme environments.

Copper removal and microbial community analysis in single-chamber microbial fuel cell.

PubMed

Wu, Yining; Zhao, Xin; Jin, Min; Li, Yan; Li, Shuai; Kong, Fanying; Nan, Jun; Wang, Aijie

2018-04-01

In this study, copper removal and electricity generation were investigated in a single-chamber microbial fuel cell (MFC). Result showed that copper was efficiently removed in the membrane-less MFC with removal efficiency of 98.3% at the tolerable Cu 2+ concentration of 12.5 mg L -1 , the corresponding open circuit voltage and maximum power density were 0.78 V and 10.2 W m -3 , respectively. The mechanism analysis demonstrated that microbial electrochemical reduction contributed to the copper removal with the products of Cu and Cu 2 O deposited at biocathode. Moreover, the microbial community analysis indicated that microbial communities changed with different copper concentrations. The dominant phyla were Proteobacteria and Bacteroidetes which could play key roles in electricity generation, while Actinobacteria and Acidobacteria were also observed which were responsible for Cu-resistant and copper removal. It will be of important guiding significance for the recovery of copper from low concentration wastewater through single-chamber MFC with simultaneous energy recovery. Copyright © 2018 Elsevier Ltd. All rights reserved.

Atmospheric Deposition-Carried Zn and Cd from a Zinc Smelter and Their Effects on Soil Microflora as Revealed by 16S rDNA

NASA Astrophysics Data System (ADS)

Shen, Feng; Li, Yanxia; Zhang, Min; Awasthi, Mukesh Kumar; Ali, Amjad; Li, Ronghua; Wang, Quan; Zhang, Zengqiang

2016-12-01

In this study, we investigated the influence of heavy metals (HM) on total soil bacterial population and its diversity pattern from 10 km distance of a Zinc smelter in Feng County, Qinling Mountain, China. We characterized and identified the bacterial community in a HM polluted soil using 16S rDNA technology. Out results indicated that the maximum soil HM concentration and the minimum bacterial population were observed in S2 soil, whereas bacterial diversity raised with the sampling distance increased. The bacterial communities were dominated by the phyla Proteobacteria, Acidobacteria and Actinobacteria in cornfield soils, except Fimicutes phylum which dominated in hilly area soil. The soil CEC, humic acid (HA)/fulvic acid (FA) and microbial OTUs increased with the sampling distance increased. Shewanella, Halomonas and Escherichia genera were highly tolerant to HM stress in both cultivated and non-cultivated soil. Finally, we found a consistent correlation of bacterial diversity with total HM and SOM along the sampling distance surrounding the zinc smelter, which could provide a new insight into the bacterial community-assisted and phytoremediation of HM contaminated soils.

SANDPUMA: ensemble predictions of nonribosomal peptide chemistry reveal biosynthetic diversity across Actinobacteria.

PubMed

Chevrette, Marc G; Aicheler, Fabian; Kohlbacher, Oliver; Currie, Cameron R; Medema, Marnix H

2017-10-15

Nonribosomally synthesized peptides (NRPs) are natural products with widespread applications in medicine and biotechnology. Many algorithms have been developed to predict the substrate specificities of nonribosomal peptide synthetase adenylation (A) domains from DNA sequences, which enables prioritization and dereplication, and integration with other data types in discovery efforts. However, insufficient training data and a lack of clarity regarding prediction quality have impeded optimal use. Here, we introduce prediCAT, a new phylogenetics-inspired algorithm, which quantitatively estimates the degree of predictability of each A-domain. We then systematically benchmarked all algorithms on a newly gathered, independent test set of 434 A-domain sequences, showing that active-site-motif-based algorithms outperform whole-domain-based methods. Subsequently, we developed SANDPUMA, a powerful ensemble algorithm, based on newly trained versions of all high-performing algorithms, which significantly outperforms individual methods. Finally, we deployed SANDPUMA in a systematic investigation of 7635 Actinobacteria genomes, suggesting that NRP chemical diversity is much higher than previously estimated. SANDPUMA has been integrated into the widely used antiSMASH biosynthetic gene cluster analysis pipeline and is also available as an open-source, standalone tool. SANDPUMA is freely available at https://bitbucket.org/chevrm/sandpuma and as a docker image at https://hub.docker.com/r/chevrm/sandpuma/ under the GNU Public License 3 (GPL3). chevrette@wisc.edu or marnix.medema@wur.nl. Supplementary data are available at Bioinformatics online. © The Author (2017). Published by Oxford University Press. All rights reserved. For Permissions, please email: journals.permissions@oup.com

Mass spectrometric approaches for the identification of anthracycline analogs produced by actinobacteria.

PubMed

Bauermeister, Anelize; Zucchi, Tiago Domingues; Moraes, Luiz Alberto Beraldo

2016-06-01

Anthracyclines are a well-known chemical class produced by actinobacteria used effectively in cancer treatment; however, these compounds are usually produced in few amounts because of being toxic against their producers. In this work, we successfully explored the mass spectrometry versatility to detect 18 anthracyclines in microbial crude extract. From collision-induced dissociation and nuclear magnetic resonance spectra, we proposed structures for five new and identified three more anthracyclines already described in the literature, nocardicyclins A and B and nothramicin. One new compound 8 (4-[4-(dimethylamino)-5-hydroxy-4,6-dimethyloxan-2-yl]oxy-2,5,7,12-tetrahydroxy-3,10-dimethoxy-2-methyl-3,4-dihydrotetracene-1,6,11-trione) was isolated and had its structure confirmed by (1) H nuclear magnetic resonance. The anthracyclines identified in this work show an interesting aminoglycoside, poorly found in natural products, 3-methyl-rhodosamine and derivatives. This fact encouraged to develop a focused method to identify compounds with aminoglycosides (rhodosamine, m/z 158; 3-methyl-rhodosamine, m/z 172; 4'-O-acethyl-3-C-methyl-rhodosamine, m/z 214). This method allowed the detection of four more anthracyclines. This focused method can also be applied in the search of these aminoglycosides in other microbial crude extracts. Additionally, it was observed that nocardicyclin A, nothramicin and compound 8 were able to interact to DNA through a DNA-binding study by mass spectrometry, showing its potential as anticancer drugs. Copyright © 2016 John Wiley & Sons, Ltd. Copyright © 2016 John Wiley & Sons, Ltd.

A glimpse of the endophytic bacterial diversity in roots of blackberry plants (Rubus fruticosus).

PubMed

Contreras, M; Loeza, P D; Villegas, J; Farias, R; Santoyo, G

2016-09-16

The aim of this study was to explore the diversity of culturable bacterial communities residing in blackberry plants (Rubus fruticosus). Bacterial endophytes were isolated from plant roots, and their 16S rDNA sequences were amplified and sequenced. Our results show that the roots of R. fruticosus exhibit low colony forming units of bacterial endophytes per gram of fresh tissue (6 x 10 2 ± 0.5 x 10 2 ). We identified 41 endophytic bacterial species in R. fruticosus by BLAST homology search and a subsequent phylogenetic analysis, belonging to the classes Actinobacteria, Bacilli, Alfaproteobacteria, Betaproteobacteria, and Gammaproteobacteria. Predominantly, genera belonging the Proteobacteria (Burkholderia, 29.4%; Herbaspirillum, 10.7%; Pseudomonas, 4.9%; and Dyella, 3.9%), Firmicutes (Bacillus, 42.1%), and Actinobacteria (two isolates showing high identity with the Streptomyces genus, 1.9%) divisions were identified. Fifty percent of the bacterial endophytes produced the phytohormone indole-acetic acid (IAA), eleven of which exhibited higher IAA production (>5.8 mg/mL) compared to the plant growth-promoting strain, Pseudomonas fluorescens UM270. Additionally, the endophytic isolates exhibited protease activity (22%), produced siderophores (26.4%), and demonstrated antagonistic action (>50% inhibition of mycelial growth) against the grey mold phytopathogen Botrytis cinerea (3.9%). These results suggested that field-grown R. fruticosus plants contain bacterial endophytes within their tissues with the potential to promote plant growth and display antagonism towards plant pathogens.

Phylogeny and bioactivity of epiphytic Gram-positive bacteria isolated from three co-occurring antarctic macroalgae.

PubMed

Alvarado, Pamela; Huang, Ying; Wang, Jian; Garrido, Ignacio; Leiva, Sergio

2018-02-19

Marine macroalgae are emerging as an untapped source of novel microbial diversity and, therefore, of new bioactive secondary metabolites. This study was aimed at assessing the diversity and antimicrobial activity of the culturable Gram-positive bacteria associated with the surface of three co-occurring Antarctic macroalgae. Specimens of Adenocystis utricularis (brown alga), Iridaea cordata (red alga) and Monostroma hariotii (green alga) were collected from the intertidal zone of King George Island, Antarctica. Gram-positive bacteria were investigated by cultivation-based methods and 16S rRNA gene sequencing, and screened for antimicrobial activity against a panel of pathogenic microorganisms. Isolates were found to belong to 12 families, with a dominance of Microbacteriaceae and Micrococcaceae. Seventeen genera of Actinobacteria and 2 of Firmicutes were cultured from the three macroalgae, containing 29 phylotypes. Three phylotypes within Actinobacteria were regarded as potentially novel species. Sixteen isolates belonging to the genera Agrococcus, Arthrobacter, Micrococcus, Pseudarthrobacter, Pseudonocardia, Sanguibacter, Staphylococcus, Streptomyces and Tessaracoccus exhibited antibiotic activity against at least one of the indicator strains. The bacterial phylotype composition was distinct among the three macroalgae species, suggesting that these macroalgae host species-specific Gram-positive associates. The results highlight the importance of Antarctic macroalgae as a rich source of Gram-positive bacterial diversity and potentially novel species, and a reservoir of bacteria producing biologically active compounds with pharmacological potential.

Sebum and Hydration Levels in Specific Regions of Human Face Significantly Predict the Nature and Diversity of Facial Skin Microbiome.

PubMed

Mukherjee, Souvik; Mitra, Rupak; Maitra, Arindam; Gupta, Satyaranjan; Kumaran, Srikala; Chakrabortty, Amit; Majumder, Partha P

2016-10-27

The skin microbiome varies across individuals. The causes of these variations are inadequately understood. We tested the hypothesis that inter-individual variation in facial skin microbiome can be significantly explained by variation in sebum and hydration levels in specific facial regions of humans. We measured sebum and hydration from forehead and cheek regions of healthy female volunteers (n = 30). Metagenomic DNA from skin swabs were sequenced for V3-V5 regions of 16S rRNA gene. Altogether, 34 phyla were identified; predominantly Actinobacteria (66.3%), Firmicutes (17.7%), Proteobacteria (13.1%) and Bacteroidetes (1.4%). About 1000 genera were identified; predominantly Propionibacterium (58.6%), Staphylococcus (8.6%), Streptococcus (4.0%), Corynebacterium (3.6%) and Paracoccus (3.3%). A subset (n = 24) of individuals were sampled two months later. Stepwise multiple regression analysis showed that cheek sebum level was the most significant predictor of microbiome composition and diversity followed by forehead hydration level; forehead sebum and cheek hydration levels were not. With increase in cheek sebum, the prevalence of Actinobacteria (p = 0.001)/Propionibacterium (p = 0.002) increased, whereas microbiome diversity decreased (Shannon Index, p = 0.032); this was opposite for other phyla/genera. These trends were reversed for forehead hydration levels. Therefore, the nature and diversity of facial skin microbiome is jointly determined by site-specific lipid and water levels in the stratum corneum.

Interspecific variations in the gastrointestinal microbiota in penguins

PubMed Central

Dewar, Meagan L; Arnould, John P Y; Dann, Peter; Trathan, Phil; Groscolas, Rene; Smith, Stuart

2013-01-01

Despite the enormous amount of data available on the importance of the gastrointestinal (GI) microbiota in vertebrate (especially mammals), information on the GI microbiota of seabirds remains incomplete. As with many seabirds, penguins have a unique digestive physiology that enables them to store large reserves of adipose tissue, protein, and lipids. This study used quantitative real-time polymerase chain reaction (qPCR) and 16S rRNA gene pyrosequencing to characterize the interspecific variations of the GI microbiota of four penguin species: the king, gentoo, macaroni, and little penguin. The qPCR results indicated that there were significant differences in the abundance of the major phyla Firmicutes, Bacteroides, Actinobacteria, and Proteobacteria. A total of 132,340, 18,336, 6324, and 4826 near full-length 16S rRNA gene sequences were amplified from fecal samples collected from king, gentoo, macaroni, and little penguins, respectively. A total of 13 phyla were identified with Firmicutes, Bacteroidetes, Proteobacteria, and Fusobacteria dominating the composition; however, there were major differences in the relative abundance of the phyla. In addition, this study documented the presence of known human pathogens, such as Campylobacter, Helicobacter, Prevotella, Veillonella, Erysipelotrichaceae, Neisseria, and Mycoplasma. However, their role in disease in penguins remains unknown. To our knowledge, this is the first study to provide an in-depth investigation of the GI microbiota of penguins. PMID:23349094

Cecal bacterial communities in wild Japanese rock ptarmigans and captive Svalbard rock ptarmigans.

PubMed

Ushida, Kazunari; Segawa, Takahiro; Tsuchida, Sayaka; Murata, Koichi

2016-02-01

Preservation of indigenous gastrointestinal microbiota is deemed to be critical for successful captive breeding of endangered wild animals, yet its biology is poorly understood. Here, we investigated cecal bacterial communities in wild Japanese rock ptarmigans (Lagopus muta japonica) and compared them with those in Svalbard rock ptarmigans (L. m. hyperborea) in captivity. Ultra-deep sequencing of 16S rRNA gene indicated that the community structure of cecal microbiota in wild rock ptarmigans was remarkably different from that in captive Svalbard rock ptarmigans. Fundamental differences between bacterial communities in the two groups of birds were detected at the phylum level. Firmicutes, Actinobacteria, Bacteroidetes and Synergistetes were the major phyla detected in wild Japanese rock ptarmigans, whereas Firmicutes alone occupied more than 80% of abundance in captive Svalbard rock ptarmigans. Furthermore, unclassified genera of Coriobacteriaceae, Synergistaceae, Bacteroidaceae, Actinomycetaceae, Veillonellaceae and Clostridiales were the major taxa detected in wild individuals, whereas in zoo-reared birds, major genera were Ruminococcus, Blautia, Faecalibacterium and Akkermansia. Zoo-reared birds seemed to lack almost all rock ptarmigan-specific bacteria in their intestine, which may explain the relatively high rate of pathogenic infections affecting them. We show evidence that preservation and reconstitution of indigenous cecal microflora are critical for successful ex situ conservation and future re-introduction plan for the Japanese rock ptarmigan.

Metagenomic survey of bacterial diversity in the atmosphere of Mexico City using different sampling methods.

PubMed

Serrano-Silva, N; Calderón-Ezquerro, M C

2018-04-01

The identification of airborne bacteria has traditionally been performed by retrieval in culture media, but the bacterial diversity in the air is underestimated using this method because many bacteria are not readily cultured. Advances in DNA sequencing technology have produced a broad knowledge of genomics and metagenomics, which can greatly improve our ability to identify and study the diversity of airborne bacteria. However, researchers are facing several challenges, particularly the efficient retrieval of low-density microorganisms from the air and the lack of standardized protocols for sample collection and processing. In this study, we tested three methods for sampling bioaerosols - a Durham-type spore trap (Durham), a seven-day recording volumetric spore trap (HST), and a high-throughput 'Jet' spore and particle sampler (Jet) - and recovered metagenomic DNA for 16S rDNA sequencing. Samples were simultaneously collected with the three devices during one week, and the sequencing libraries were analyzed. A simple and efficient method for collecting bioaerosols and extracting good quality DNA for high-throughput sequencing was standardized. The Durham sampler collected preferentially Cyanobacteria, the HST Actinobacteria, Proteobacteria and Firmicutes, and the Jet mainly Proteobacteria and Firmicutes. The HST sampler collected the largest amount of airborne bacterial diversity. More experiments are necessary to select the right sampler, depending on study objectives, which may require monitoring and collecting specific airborne bacteria. Copyright © 2017 Elsevier Ltd. All rights reserved.