Abstract
Bacterioplankton dynamics at Helgoland Roads (54°11.3′N, 7°54.0′E) in the North Sea over the winter–spring transition were investigated. The bacterial community was analyzed and correlated ...with phytoplankton community data and abiotic parameters. The community structure was analyzed by ribosomal intergenic spacer analysis (RISA) and by denaturing gradient gel electrophoresis (DGGE) of 16S rRNA genes followed by DNA sequence analysis. The linkage of abiotic and biotic environmental factors and bacterial community as well as phylotypes (sequenced DGGE bands) was analyzed by the ordination technique of canonical correspondence analysis (CCA). Generally, an influence of temperature and phytoplankton on the bacterial community during the sampling period was observed. Additionally, multivariate analysis by factors revealed an influence on specific bacterial phylotypes of these factors. Overall, results indicate that changes in the bacterial community were caused not only by abiotic factors but also by the phytoplankton community.
Specific associations of bacteria with phytoplankton have recently been reported in the literature. In our study, we analyzed bacterial communities of microalgal cultures related to algal growth ...phases. Seven freshly isolated key diatom and dinoflagellate species from Helgoland Roads, North Sea, were investigated. The community composition of associated bacteria as well as the cell numbers, the photosynthetic efficiency of the algae, and the depletion of inorganic nutrients in the medium were recorded over a period of 8 weeks in batch cultures. Diversity and succession of bacterial communities was analyzed by ribosomal intergenic spacer analysis. Phylogenetic analysis of bacterial populations was performed by denaturing gradient gel electrophoresis of 16S rRNA genes followed by DNA sequence analysis. Members of Alphaproteobacteria and Gammaproteobacteria and the Flavobacteria-Sphingobacteria group within the Bacteroidetes phylum predominated in the cultures. Differences in free-living and attached bacterial populations were observed between the phylogenetic groups. Shifts in the bacterial communities could not be correlated to changes of nutrient levels or algal growth phases. Regarding our results, it should not be generalized that the compositions of the bacterial communities are strictly species specific for microalgae. The importance of factors like the composition of exudates is apparent.
Common bacterial blight is a devastating seed-borne disease of common beans that also occurs on other legume species including lablab and Lima beans. We sequenced and analyzed the genomes of 26 ...strains of Xanthomonas axonopodis pv. phaseoli and X. fuscans subsp. fuscans, the causative agents of this disease, collected over four decades and six continents. This revealed considerable genetic variation within both taxa, encompassing both single-nucleotide variants and differences in gene content, that could be exploited for tracking pathogen spread. The bacterial strain from Lima bean fell within the previously described Genetic Lineage 1, along with the pathovar type strain (NCPPB 3035). The strains from lablab represent a new, previously unknown genetic lineage closely related to strains of X. axonopodis pv. glycines. Finally, we identified more than 100 genes that appear to have been recently acquired by Xanthomonas axonopodis pv. phaseoli from X. fuscans subsp. fuscans.
Knowledge on the spatial distribution of prokaryotic taxa is an essential basis to understand microbial diversity and the factors shaping its patterns. Large-scale patterns of faunal distribution are ...thought to be influenced by physical environmental factors, whereas smaller scale spatial heterogeneity is maintained by species-specific life-history characteristics, the quantity and quality of food sources and local disturbances including both natural and man-induced events. However, it is still not clear which environmental parameters control the diversity and community structure of sedimentary microorganisms mediating important ecosystem processes. In this study, multiscale patterns were elucidated at seven stations in the Oyster Ground, North Sea (54°4′N/4°E), 100 m to 11 km apart. These were related to biotic (e.g. multicellular organisms) and abiotic parameters (e.g. organic carbon content in the sediment) to establish the relationship between the distribution of both bacterial and archaeal communities and their environment. A relatively high variability was detected at all scales for bacterial and archaeal communities, both of which were controlled by different suites of biotic and abiotic environmental variables. The bacterial community consisted mainly of members belonging to the Gammaproteobacteria and the Fibrobacteres/Acidobacteria group. Members of the Deltaproteobacteria, Bacteroidetes and Actinobacteria also contributed to the bacterial community. Euryarchaeota formed the majority of archaeal phylotypes together with three phylotypes belonging to the Crenarchaeota.
We announce the genome sequence for Xanthomonas species strain Nyagatare, isolated from beans showing unusual disease symptoms in Rwanda. This strain represents the first sequenced genome belonging ...to an as-yet undescribed Xanthomonas species known as species-level clade 1. It has at least 100 kb of genomic sequence that shows little or no sequence similarity to other xanthomonads, including a unique lipopolysaccharide synthesis gene cluster. At least one genomic region appears to have been acquired from relatives of Agrobacterium or Rhizobium species. The genome encodes homologues of only three known type-three secretion system effectors: AvrBs2, XopF1 and AvrXv4. Availability of the genome sequence will facilitate development of molecular tools for detection and diagnostics for this newly discovered pathogen of beans and facilitate epidemiological investigations of a potential causal link between this pathogen and the disease outbreak.
We present the genome sequence of the Nyagatare strain, a bacterial pathogen on beans that may be responsible for a mysterious disease emerging in Rwanda.
Little is currently known about the potential impact of silver nanoparticles (AgNPs) on estuarine microbial communities. The Colne estuary, UK, is susceptible to oil pollution through boat traffic, ...and there is the potential for AgNP exposure via effluent discharged from a sewage treatment works located in close proximity. This study examined the effects of uncapped AgNPs (uAgNPs), capped AgNPs (cAgNPs) and dissolved Ag2SO4, on hydrocarbon-degrading microbial communities in estuarine sediments. The uAgNPs, cAgNPs and Ag2SO4 (up to 50 mg L−1) had no significant impact on hydrocarbon biodegradation (80–92% hydrocarbons were biodegraded by day 7 in all samples). Although total and active cell counts in oil-amended sediments were unaffected by silver exposure; total cell counts in non-oiled sediments decreased from 1.66 to 0.84 × 107 g−1 dry weight sediment (dws) with 50 mg L−1 cAgNPs and from 1.66 to 0.66 × 107 g−1 dws with 0.5 mg L−1 Ag2SO4 by day 14. All silver-exposed sediments also underwent significant shifts in bacterial community structure, and one DGGE band corresponding to a member of Bacteroidetes was more prominent in non-oiled microcosms exposed to 50 mg L−1 Ag2SO4 compared to non-silver controls. In conclusion, AgNPs do not appear to affect microbial hydrocarbon-degradation but do impact on bacterial community diversity, which may have potential implications for other important microbial-mediated processes in estuaries.
•Microbial hydrocarbon biodegradation was not impacted by up to 50 mg L−1 AgNPs.•50 mg L−1 cAgNPs caused a significant reduction in sediment cell counts by day 14.•0.5 mg L−1 Ag2SO4 caused a significant reduction in sediment cell counts by day 14.•Cell counts in oil-amended sediments were not affected by AgNPs or Ag2SO4.•Microbial community structures were impacted by all types and concentrations of Ag.
Nematodes represent a species-rich and morphologically diverse group of metazoans known to inhabit both aquatic and terrestrial environments. Their role as biological indicators and as key players in ...nutrient cycling has been well documented. Some plant-parasitic species are also known to cause significant losses to crop production. In spite of this, there still exists a huge gap in our knowledge of their diversity due to the enormity of time and expertise often involved in characterising species using phenotypic features. Molecular methodology provides useful means of complementing the limited number of reliable diagnostic characters available for morphology-based identification. We discuss herein some of the limitations of traditional taxonomy and how molecular methodologies, especially the use of high-throughput sequencing, have assisted in carrying out large-scale nematode community studies and characterisation of phytonematodes through rapid identification of multiple taxa. We also provide brief descriptions of some the current and almost-outdated high-throughput sequencing platforms and their applications in both plant nematology and soil ecology.
Objectives The marine benthic nitrogen cycle is affected by both the presence and activity of macrofauna and the diversity of N-cycling microbes. However, integrated research simultaneously ...investigating macrofauna, microbes and N-cycling is lacking. We investigated spatio-temporal patterns in microbial community composition and diversity, macrofaunal abundance and their sediment reworking activity, and N-cycling in seven subtidal stations in the Southern North Sea. Spatio-Temporal Patterns of the Microbial Communities Our results indicated that bacteria (total and beta -AOB) showed more spatio-temporal variation than archaea (total and AOA) as sedimentation of organic matter and the subsequent changes in the environment had a stronger impact on their community composition and diversity indices in our study area. However, spatio-temporal patterns of total bacterial and beta -AOB communities were different and related to the availability of ammonium for the autotrophic beta -AOB. Highest bacterial richness and diversity were observed in June at the timing of the phytoplankton bloom deposition, while richness of beta -AOB as well as AOA peaked in September. Total archaeal community showed no temporal variation in diversity indices. Macrofauna, Microbes and the Benthic N-Cycle Distance based linear models revealed that, independent from the effect of grain size and the quality and quantity of sediment organic matter, nitrification and N-mineralization were affected by respectively the diversity of metabolically active beta -AOB and AOA, and the total bacteria, near the sediment-water interface. Separate models demonstrated a significant and independent effect of macrofaunal activities on community composition and richness of total bacteria, and diversity indices of metabolically active AOA. Diversity of beta -AOB was significantly affected by macrofaunal abundance. Our results support the link between microbial biodiversity and ecosystem functioning in marine sediments, and provided broad correlative support for the hypothesis that this relationship is modulated by macrofaunal activity. We hypothesized that the latter effect can be explained by their bioturbating and bio-irrigating activities, increasing the spatial complexity of the biogeochemical environment.
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Dostopno za:
DOBA, IZUM, KILJ, NUK, PILJ, PNG, SAZU, SIK, UILJ, UKNU, UL, UM, UPUK
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