Actinomycete-flora associated with submersed freshwater macrophytes

Meiofauna promotes litter decomposition in stream ecosystems depending on leaf species

Litter decomposition, a fundamental process of nutrient cycling and energy flow in freshwater ecosystems, is driven by a diverse array of decomposers. As an important component of the heterotrophic food web, meiofauna can provide a trophic link between leaf-associated microbes (i.e., bacteria and fungi)/plant detritus and macroinvertebrates, though their contribution to litter decomposition is not well understood. To investigate the role of different decomposer communities in litter decomposition, especially meiofauna, we compared the litter decomposition of three leaf species with different lignin to nitrogen ratios in litter bags with different mesh sizes (0.05, 0.25, and 2 mm) in a forested stream, in China for 78 days. The meiofauna significantly enhanced the decomposition of leaves of high-and medium- quality, while decreasing (negative effect) or increasing (positive effect) the fungal biomass and diversity. Macrofauna and meiofauna together contributed to the decomposition of low-quality leaf species. The presence of meiofauna and macrofauna triggered different aspects of the microbial community, with their effects on litter decomposition varying as a function of leaf quality. This study reveals that the meiofauna increased the trophic complexity and modulated their interactions with microbes, highlighting the important yet underestimated role of meiofauna in detritus-based ecosystems.

Determinants of Soil Bacterial and Fungal Community Composition Toward Carbon-Use Efficiency Across Primary and Secondary Forests in a Costa Rican Conservation Area

Tropical secondary forests currently represent over half of the world's remaining tropical forests and are critical candidates for maintaining global biodiversity and enhancing potential carbon-use efficiency (CUE) and, thus, carbon sequestration. However, these ecosystems can exhibit multiple successional pathways, which have hindered our understanding of the soil microbial drivers that facilitate improved CUE. To begin to address this, we examined soil % C; % N; C:N ratio; soil microbial biomass C (C_mic); NO₃^-; NH₄⁺; pH; % moisture; % sand, silt, and clay; and elevation, along with soil bacterial and fungal community composition, and determined which soil abiotic properties structure the soil C_mic and the soil bacterial and fungal communities across a primary forest, 33-year-old secondary forest, and 22-year-old young secondary in the Northern Zone of Costa Rica. We provide evidence that soil microbial communities were mostly distinct across the habitat types and that these habitats appear to have affected the soil ectomycorrhizal fungi and the soil microbial groups associated with the degradation of complex carbon compounds. We found that soil C_mic levels increased along the management gradient from young, to old secondary, to primary forest. In addition, the changes in soil C_mic and soil fungal community structure were significantly related to levels of soil NO₃^-. Our analyses showed that even after 33 years of natural forest regrowth, the clearing of tropical forests can have persistent effects on soil microbial communities and that it may take a longer time than we realized for secondary forests to develop carbon-utilization efficiencies similar to that of a primary forest. Our results also indicated that forms of inorganic N may be an important factor in structuring soil C_mic and the soil microbial communities, leading to improved CUE in regenerating secondary forests. This study is the first in the region to highlight some of the factors which appear to be structuring the soil C_mic and soil microbial communities such that they are more conducive for enhanced CUE in secondary forests.

Chitinolytic functions in actinobacteria: ecology, enzymes, and evolution

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.

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

BACKGROUND

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.

RESULTS

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.

CONCLUSION

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.

Assessing the effect of litter species on the dynamic of bacterial and fungal communities during leaf decomposition in microcosm by molecular techniques

Although bacteria and fungi are well-known to be decomposers of leaf litter, few studies have examined their compositions and diversities during the decomposition process in tropical stream water. Xishuangbanna is a tropical region preserving one of the highest floristic diversity areas in China. In this study, leaf litter of four dominant plant species in Xishuangbanna was incubated in stream water for 42 days during which samples were taken regularly. Following DNA extraction, PCR-DGGE (denaturing gradient gel electrophoresis) and clone-sequencing analyses were performed using bacterial and fungal specific primers. Leaf species have slightly influences on bacterial community rather than fungal community. The richness and diversity of bacteria was higher than that of fungi, which increased towards the end of the 42-day-incubation. The bacterial community was initially more specific upon the type of leaves and gradually became similar at the later stage of decomposition with alpha-proteobacteria as major component. Sequences affiliated to methanotrophs were obtained that indicates potentially occurrence of methane oxidation and methanogenesis. For the fungal community, sequences affiliated to Aspergillus were predominant at the beginning and then shifted to Pleosporales. Our results suggest that the microorganisms colonizing leaf biofilm in tropical stream water were mostly generalists that could exploit the resources of leaves of various species equally well.

Chemolithotrophic nitrate-dependent Fe(II)-oxidizing nature of actinobacterial subdivision lineage TM3

Anaerobic nitrate-dependent Fe(II) oxidation is widespread in various environments and is known to be performed by both heterotrophic and autotrophic microorganisms. Although Fe(II) oxidation is predominantly biological under acidic conditions, to date most of the studies on nitrate-dependent Fe(II) oxidation were from environments of circumneutral pH. The present study was conducted in Lake Grosse Fuchskuhle, a moderately acidic ecosystem receiving humic acids from an adjacent bog, with the objective of identifying, characterizing and enumerating the microorganisms responsible for this process. The incubations of sediment under chemolithotrophic nitrate-dependent Fe(II)-oxidizing conditions have shown the enrichment of TM3 group of uncultured Actinobacteria. A time-course experiment done on these Actinobacteria showed a consumption of Fe(II) and nitrate in accordance with the expected stoichiometry (1:0.2) required for nitrate-dependent Fe(II) oxidation. Quantifications done by most probable number showed the presence of 1 × 10(4) autotrophic and 1 × 10(7) heterotrophic nitrate-dependent Fe(II) oxidizers per gram fresh weight of sediment. The analysis of microbial community by 16S rRNA gene amplicon pyrosequencing showed that these actinobacterial sequences correspond to ~0.6% of bacterial 16S rRNA gene sequences. Stable isotope probing using (13)CO2 was performed with the lake sediment and showed labeling of these Actinobacteria. This indicated that they might be important autotrophs in this environment. Although these Actinobacteria are not dominant members of the sediment microbial community, they could be of functional significance due to their contribution to the regeneration of Fe(III), which has a critical role as an electron acceptor for anaerobic microorganisms mineralizing sediment organic matter. To the best of our knowledge this is the first study to show the autotrophic nitrate-dependent Fe(II)-oxidizing nature of TM3 group of uncultured Actinobacteria.

Phylogenetic diversity of bacterial communities inhabiting the sediment of Lake Hévíz - a comparison of cultivation and cloning

Lake Hévíz is the largest natural warm water lake of Europe. The curative mud of the lake comprises volcanic and marsh components although their species composition is hardly known yet. The aim of the present study was to gain information about the distribution and species diversity of bacterial communities inhabiting the sediment of Lake Hévíz using cultivation-based and molecular cloning methods. Samples from two depths and locations were taken in 2004 and 2007. Representatives of the altogether 255 bacterial isolates were affiliated with the phyla Firmicutes, Actinobacteria, Proteobacteria and Bacteroidetes. The most abundant groups belonged to the genus Bacillus (Firmicutes). Many of Lake Hévíz isolates showed the highest sequence similarity to bacteria known to be plant associated or members of normal human microbiota as well as participating in decomposition of highly resistant organic materials. In the three clone libraries, phylotypes belonging to altogether different phyla (Firmicutes, Actinobacteria, Proteobacteria, Bacteroidetes, Cyanobacteria, Chlorobi, Chloroflexi, Deferribacteres, Nitrospirae, Spirochaetes and Verrucomicrobia) were revealed from which members of Gammaproteobacteria and Cyanobacteria proved to be the most abundant. Regardless of the sampling times and methodology used, high spatial heterogeneities of bacterial community structures were characteristic of the sediment of Lake Hévíz.

Proteomic and physiological responses of Kineococcus radiotolerans to copper

Copper is a highly reactive, toxic metal; consequently, transport of this metal within the cell is tightly regulated. Intriguingly, the actinobacterium Kineococcus radiotolerans has been shown to not only accumulate soluble copper to high levels within the cytoplasm, but the phenotype also correlated with enhanced cell growth during chronic exposure to ionizing radiation. This study offers a first glimpse into the physiological and proteomic responses of K. radiotolerans to copper at increasing concentration and distinct growth phases. Aerobic growth rates and biomass yields were similar over a range of Cu(II) concentrations (0–1.5 mM) in complex medium. Copper uptake coincided with active cell growth and intracellular accumulation was positively correlated with Cu(II) concentration in the growth medium (R² = 0.7). Approximately 40% of protein coding ORFs on the K. radiotolerans genome were differentially expressed in response to the copper treatments imposed. Copper accumulation coincided with increased abundance of proteins involved in oxidative stress and defense, DNA stabilization and repair, and protein turnover. Interestingly, the specific activity of superoxide dismutase was repressed by low to moderate concentrations of copper during exponential growth, and activity was unresponsive to perturbation with paraquot. The biochemical response pathways invoked by sub-lethal copper concentrations are exceptionally complex; though integral cellular functions are preserved, in part, through the coordination of defense enzymes, chaperones, antioxidants and protective osmolytes that likely help maintain cellular redox. This study extends our understanding of the ecology and physiology of this unique actinobacterium that could potentially inspire new biotechnologies in metal recovery and sequestration, and environmental restoration.

A polyphasic study on the species diversity of the sediment microbiota of Lake Hévíz

Lake Hévíz is the largest natural thermal lake of Europe, harboring special bacterial communities. The aim of the present study was to gain information about the distribution and species diversity of the sediment microbiota, with special focus on Actinobacteria, by using cultivation-based and -independent molecular methods. Samples from two depths were taken in two different locations in October 2007. 245 strains were isolated, grouped to 85 OTUs by ARDRA, and identified by 16S rDNA sequencing. Most of the strains showed highest sequence similarity with Bacillus and related genera. Strains belonging to the phylum Actinobacteria were identified as members of Arthrobacter, Brachybacterium, Brevibacterium, Curtobacterium, Friedmanniella, Gordonia, Kocuria, Microbacterium, Micrococcus, Micromonospora, Mycobacterium, Rhodococcus, Streptomyces and Williamsia . Two clone libraries were constructed from H3M and H4M samples, providing 288 and 192 clones which were grouped to 150 and 125 OTUs, respectively, by ARDRA. The two most abundant group of the H4M library were OP8-related. The phylum Proteobacteria was represented mostly by delta-Proteobacteria, other relevant groups were Cyanobacteria, Bacteroidetes, Acidobacteria and beta-Proteobacteria. The H3M library was dominated by Cyanobacteria, Verrucomicrobia, beta-Proteobacteria, gamma-Proteobacteria and delta-Proteobacteria. Chloroflexi, Bacteroidetes, Spirochetes and Firmicutes were scarce. Results from the clone libraries were compared to the length-heterogeneity-PCR fingerprints of the communities.

In vitro and in vivo antagonism of actinomycetes isolated from Moroccan rhizospherical soils against Sclerotium rolfsii: a causal agent of root rot on sugar beet (Beta vulgaris L.)

AIMS

To evaluate the ability of the isolated actinomycetes to inhibit in vitro plant pathogenic fungi and the efficacy of promising antagonistic isolates to reduce in vivo the incidence of root rot induced by Sclerotium rolfsii on sugar beet.

METHODS AND RESULTS

Actinomycetes isolated from rhizosphere soil of sugar beet were screened for antagonistic activity against a number of plant pathogens, including S. rolfsii. Ten actinomycetes out of 195 screened in vitro were strongly inhibitory to S. rolfsii. These isolates were subsequently tested for their ability to inhibit sclerotial germination and hyphal growth of S. roflsii. The most important inhibitions were obtained by the culture filtrate from the isolates J-2 and B-11, including 100% inhibition of sclerotial germination and 80% inhibition of hyphal growth. These two isolates (J-2 and B-11) were then screened for their ability to protect sugar beet against infection of S. rolfsii induced root rot in a pot trial. The treatment of S. rolfsii infested soil with a biomass and culture filtrate mixture of the selected antagonists reduced significantly (P < or = 0.05) the incidence of root rot on sugar beet. Isolate J-2 was most effective and allowed a high fresh weight of sugar beet roots to be obtained. Both antagonists J-2 and B-11 were classified as belonging to the genus Streptomyces species through morphological and chemical characteristics as well as 16S rDNA analysis.

CONCLUSION

Streptomyces isolates J-2 and B-11 showed a potential for controlling root rot on sugar beet and could be useful in integrated control against diverse soil borne plant pathogens.

SIGNIFICANCE AND IMPACT OF THE STUDY

This investigation showed the role, which actinomycete bacteria can play to control root rot caused by S. rolfsii, in the objective to reduce treatments with chemical fungicides.

Cellulose degradation by micromonosporas recovered from freshwater lakes and classification of these actinomycetes by DNA gyrase B gene sequencing

A number of Micromonospora strains isolated from the water column, sediment, and cellulose baits placed in freshwater lakes were shown to be able to degrade cellulose in lake water without any addition of nutrients. A selective isolation method was also developed to demonstrate that CFU arose from both spores and hyphae that inhabit the lake environment. Gyrase B gene sequencing performed on the isolates identified a number of new centers of variation within Micromonospora, but the most actively cellulolytic strains were recovered in a single cluster that equated with the type species of the genus, M. chalcea.

Development of a 16S rRNA gene-based prototype microarray for the detection of selected actinomycetes genera

Actinomycetes are known for their secondary metabolites, which have been successfully used as drugs in human and veterinary medicines. However, information on the distribution of this group of Gram-positive bacteria in diverse ecosystems and a comprehension of their activities in ecosystem processes are still scarce. We have developed a 16S rRNA-based taxonomic microarray that targets key actinomycetes at the genus level. In total, 113 actinomycete 16S rRNA probes, corresponding to 55 of the 202 described genera, were designed. The microarray accuracy was evaluated by comparing signal intensities with probe/target-weighted mismatch values and the Gibbs energy of the probe/target duplex formation by hybridizing 17 non-actinomycete and 29 actinomycete strains/clones with the probe set. The validation proved that the probe set was specific, with only 1.3% of false results. The incomplete coverage of actinomycetes by a genus-specific probe was caused by the limited number of 16S rRNA gene sequences in databases or insufficient 16S rRNA gene polymorphism. The microarray enabled discrimination between actinomycete communities from three forest soil samples collected at one site. Cloning and sequencing of 16S rRNA genes from one of the soil samples confirmed the microarray results. We propose that this newly constructed microarray will be a valuable tool for genus-level comparisons of actinomycete communities in various ecological conditions.

Diversity of fungi, bacteria, and actinomycetes on leaves decomposing in a stream

Although fungi, bacteria, and specific bacterial taxa, such as the actinomycetes, have been studied extensively in various habitats, few studies have examined them simultaneously, especially on decomposing leaves in streams. In this study, sugar maple and white oak leaves were incubated in a stream in northeastern Ohio for 181 days during which samples were collected at regular intervals. Following DNA extraction, PCR-denaturing gradient gel electrophoresis (DGGE) was performed using fungus-, bacterium-, and actinomycete-specific primers. In addition, fungal and bacterial biomass was estimated. Fungal biomass differed on different days but not between leaves of the two species and was always greater than bacterial biomass. There were significant differences in bacterial biomass through time and between leaf types on some days. Generally, on the basis of DGGE, few differences in community structure were found for different leaf types. However, the ribotype richness of fungi was significantly greater than those of the bacteria and actinomycetes, which were similar to each other. Ribotype richness decreased toward the end of the study for each group except bacteria. Lack of differences between the two leaf types suggests that the microorganisms colonizing the leaf biofilm were primarily generalists that could exploit the resources of the leaves of either species equally well. Thus, we conclude that factors, such as the ecological role of the taxa (generalists versus specialists), stage of decay, and time of exposure, appeared to be more important determinants of microbial community structure than leaf quality.

Actinomycetes in relation to taste and odour in drinking water: myths, tenets and truths

Actinomycetes are a complex group of bacteria present in a wide variety of environments, either as dormant spores or actively growing. Some actinomycetes produce two potent terpenoids (geosmin and 2-methylisoborneol (MIB)) and pyrazines, common causes of drinking water off flavours, and have been implicated in taste and odour episodes. However, isolation from a water source is not evidence that actinomycetes caused a taste and odour event. Dormant spores of actinomycetes may be isolated from aquatic environments in high concentrations, despite production in the terrestrial environment. Similarly, odourous compounds produced by actinomycetes may be produced terrestrially and washed into aquatic environments, with or without the actinomycetes that produced them. Actinomycetes may exist as actively growing mycelium in small, specialized habitats within an aquatic system, but their odourous compounds may influence a wider area. This paper attempts to elucidate the types and activities of actinomycetes that may be found in, or interact with, drinking water supplies.

Diversity of antifungal actinomycetes in various vegetative soils of Korea

Diversity of actinomycetes and their antifungal activities against some plant pathogenic fungi were examined in various vegetative soils from 14 different sites in the western part of Korea. Actinomycete counts ranged from 1.17 x 10(6) to 4.20 x 10(6) cfu x g(-1) dried soil. A total of 1510 actinomycetes were isolated from the soil samples. Streptomyces was predominant in soils with a pH range of 5.1-6.5, 9.1-13.0% moisture, and 9.1-11.0% organic matter. Most Micromonospora, Dactylosporangium, and Streptosporangium were distributed in soils with pH 4.0-5.0, 2.0-9.0% moisture, and 4.0-7.0% organic matter. Actinomadura and nocardioform actinomycetes were abundant in soils with pH 4.0-5.0 and 13.1-20.0% moisture and with 9.1-11.0 and 4.0-7.0% organic matter, respectively. Populations of Streptomyces were predominant in all the soils, but were highest in grassland and lowest in mountain-forest soils. Micromonospora was most abundant in pepper-field soil and nocardioform actinomycetes were highest in rice paddy field soil. Dactylosporangium was predominant in lake-mud sediments and pepper-field soil, Streptosporangium in lake-mud sediments, and Actinomadura in mountain-forest soil. Antifungal actinomycetes were abundant in orchard soil and lake mud. More than 50% of antifungal isolates from most soils were classified as genus Streptomyces. Actinomycete isolates that showed strong antifungal activity against Alternaria mali, Colletotrichum gloeosporioides, Fusarium oxysporum f.sp. cucumerinum, and Rhizoctonia solani were predominant in pepper-field soils, whereas those against Magnaporthe grisea and Phytophthora capsici were abundant in radish-field soils.