Multitrophic interactions among Western Corn Rootworm, Glomus intraradices and microbial communities in the rhizosphere and endorhiza of maize

The complex interactions among the maize pest Western Corn Rootworm (WCR), Glomus intraradices (GI-recently renamed Rhizophagus intraradices) and the microbial communities in both rhizosphere and endorhiza of maize have been investigated in view of new pest control strategies. In a greenhouse experiment, different maize treatments were established: C (control plants), W (plants inoculated with WCR), G (plants inoculated with GI), GW (plants inoculated with GI and WCR). After 20 days of WCR root feeding, larval fitness was measured. Dominant arbuscular mycorrhizal fungi (AMF) in soil and maize endorhiza were analyzed by cloning of 18S rRNA gene fragments of AMF, restriction fragment length polymorphism and sequencing. Bacterial and fungal communities in the rhizosphere and endorhiza were investigated by denaturing gradient gel electrophoresis of 16S rRNA gene and ITS fragments, PCR amplified from total community DNA, respectively. GI reduced significantly WCR larval development and affected the naturally occurring endorhiza AMF and bacteria. WCR root feeding influenced the endorhiza bacteria as well. GI can be used in integrated pest management programs, rendering WCR larvae more susceptible to predation by natural enemies. The mechanisms behind the interaction between GI and WCR remain unknown. However, our data suggested that GI might act indirectly via plant-mediated mechanisms influencing the endorhiza microbial communities

Using the class 1 integron-integrase gene as a proxy for anthropogenic pollution

This is the final version of the article. Available from the publisher via the DOI in this record.Around all human activity, there are zones of pollution with pesticides, heavy metals, pharmaceuticals, personal care products and the microorganisms associated with human waste streams and agriculture. This diversity of pollutants, whose concentration varies spatially and temporally, is a major challenge for monitoring. Here, we suggest that the relative abundance of the clinical class 1 integron-integrase gene, intI1, is a good proxy for pollution because: (1) intI1 is linked to genes conferring resistance to antibiotics, disinfectants and heavy metals; (2) it is found in a wide variety of pathogenic and nonpathogenic bacteria; (3) its abundance can change rapidly because its host cells can have rapid generation times and it can move between bacteria by horizontal gene transfer; and (4) a single DNA sequence variant of intI1 is now found on a wide diversity of xenogenetic elements, these being complex mosaic DNA elements fixed through the agency of human selection. Here we review the literature examining the relationship between anthropogenic impacts and the abundance of intI1, and outline an approach by which intI1 could serve as a proxy for anthropogenic pollution.MRG is supported by the Australian Research Council, AP is supported by the Alfred P Sloan Foundation Microbiology of the Built Environment program and the National Science Foundation RAPID award no. 1402651, KS is supported by the Deutsche Forschungsgemeinschaft (DFG) funding the Research Unit FOR 566 ‘Veterinary Medicines in Soil: Basic Research for Risk Analysis’ (Grant No. SM59/5-3) and by the Umweltbundesamt (3713 63 402), JMT is supported by the US National Science Foundation and Y-GZ is supported by the National Science Foundation of China

Biologische Bodenentseuchung für eine umweltgerechte und intensive Gehölzproduktion

Der wiederholte Nachbau von Gehölzen der Familie der Rosaceae führt zu einer Nachbaukrankheit, die als Bodenmüdigkeit beschrieben wird. Eine wirksame Bekämpfung der Bodenmüdigkeit war die chemische Desinfektion mit Basamid® Granulat, basierend auf der Freisetzung eines Isothiocyanates (ITC). Die Zulassung von Basamid® Granulat ist in Deutschland abgelaufen. Eine Alternative könnte die Biofumigation darstellen. Bei der Biofumigation werden Glucosinolat(GS)-haltige Pflanzenteile von Vertretern der Brassicaceae in den Boden eingearbeitet. Die toxischen GS-Abbauprodukte, vor allem ITC, führen zu einer biologischen Bodendesinfektion. In dem berichteten Projekt wurde die Wirkung der ein- und zweijährigen Biofumigation von Brassica juncea und Raphanus sativus mit dem Anbau von Tagetes patula NEMAMIX, der Anwendung von Basamid® Granulat und des fortgesetzten Nachbaus der Indikatorpflanzen Malus sylvestris ‘Bittenfelder, Malus M4 bzw. M106 und Rosa corymbifera ‘Laxa’ verglichen. Das beste Wachstum der Indikatorpflanzen erbrachte ein vorausgegangener, zweijähriger Anbau von Tagetes patula NEMAMIX. Die praxisübliche Anwendung von Basamid® Granulat zeigte wenig Wirkung. Vermutlich war der Boden zum Anwendungstermin zu trocken. Eine geringe Wirkung erbrachte auch die ein- oder auch zweijährige Biofumigation mit Brassica juncea und Raphanus sativus. Auch die im Rahmen der Projektverlängerung zusätzlich geprüfte Einarbeitung von Brassica juncea-Samenmehl, die Verwendung der speziellen Saatgutmischung viterra®BIOFUMIGATION zur klassischen Biofumigation sowie die Dämpfung des Bodens mit Hilfe des CombiMIXERs an zwei nachbaukranken Baumschulstandorten brachten nicht die erhofften positive Effekte auf das Pflanzenwachstum der Indikatorpflanzen. Wieder war die einjährige Kultur von Tagetes die erfolgreichste Var. im Vergleich zum unbehandelten nachbaukranken Boden. Es konnten nur wenig positive Effekte auf das Wachstum der Indikatorpflanzen statistisch gesichert werden. Selbst in den Fällen, in denen signifikante Unterschiede auftraten, reichten diese Effekte aus Sicht der Praxis bei weitem nicht aus, um die durch Minderwuchs entstehenden Ertragsverluste auszugleichen. Mögliche Gründe für die schlechte Wirkung der geprüften Varianten werden diskutiert

The impact of resource dependence of the mechanisms of life on the spatial population dynamics of an in silico microbial community

Biodiversity has a critical impact on ecosystem functionality and stability, and thus the current biodiversity crisis has motivated many studies of the mechanisms that sustain biodiversity, a notable example being non-transitive or cyclic competition. We therefore extend existing microscopic models of communities with cyclic competition by incorporating resource dependence in demographic processes, characteristics of natural systems often oversimplified or overlooked by modellers. The spatially explicit nature of our individual-based model of three interacting species results in the formation of stable spatial structures, which have significant effects on community functioning, in agreement with experimental observations of pattern formation in microbial communities. Published by AIP Publishing

PCR-based detection of mobile genetic elements in total community DNA

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Mangrove microniches determine the structural and functional diversity of enriched petroleum hydrocarbon-degrading consortia

In this study, the combination of culture enrichments and molecular tools was used to identify bacterial guilds, plasmids and functional genes potentially important in the process of petroleum hydrocarbon (PH) decontamination in mangrove microniches (rhizospheres and bulk sediment). In addition, we aimed to recover PH-degrading consortia (PHDC) for future use in remediation strategies. The PHDC were enriched with petroleum from rhizosphere and bulk sediment samples taken from a mangrove chronically polluted with oil hydrocarbons. Southern blot hybridization (SBH) assays of PCR amplicons from environmental DNA before enrichments resulted in weak positive signals for the functional gene types targeted, suggesting that PH-degrading genotypes and plasmids were in low abundance in the rhizosphere and bulk sediments. However, after enrichment, these genes were detected and strong microniche-dependent differences in the abundance and composition of hydrocarbonoclastic bacterial populations, plasmids (IncP-1 alpha, IncP-1 beta, IncP-7 and IncP-9) and functional genes (naphthalene, extradiol and intradiol dioxygenases) were revealed by in-depth molecular analyses [PCR-denaturing gradient gel electrophoresis and hybridization (SBH and microarray)]. Our results suggest that, despite the low abundance of PH-degrading genes and plasmids in the environmental samples, the original bacterial composition of the mangrove microniches determined the structural and functional diversity of the PHDC enriched.Deutsche Forschungsgemeinschaft [SM59/4-1, 4-2]; FAPERJ-Brazil; European Commission [003998, 211684]; Alexander-von-Humboldt-Stiftung; CONICET (Argentina)info:eu-repo/semantics/publishedVersio

Meeting report : 1st international functional metagenomics workshop May 7–8, 2012, St. Jacobs, Ontario, Canada

This report summarizes the events of the 1st International Functional Metagenomics Workshop. The workshop was held on May 7 and 8 in St. Jacobs, Ontario, Canada and was focused on building a core international functional metagenomics community, exploring strategic research areas, and identifying opportunities for future collaboration and funding. The workshop was initiated by researchers at the University of Waterloo with support from the Ontario Genomics Institute (OGI), Natural Sciences and Engineering Research Council of Canada (NSERC) and the University of Waterloo

Impact of shortened crop rotation of oilseed rape on soil and rhizosphere microbial diversity in relation to yield decline

Oilseed rape (OSR) grown in monoculture shows a decline in yield relative to virgin OSR of up to 25%, but the mechanisms responsible are unknown. A long term field experiment of OSR grown in a range of rotations with wheat was used to determine whether shifts in fungal and bacterial populations of the rhizosphere and bulk soil were associated with the development of OSR yield decline. The communities of fungi and bacteria in the rhizosphere and bulk soil from the field experiment were profiled using terminal restriction fragment length polymorphism (TRFLP) and sequencing of cloned internal transcribed spacer regions and 16S rRNA genes, respectively. OSR cropping frequency had no effect on rhizosphere bacterial communities. However, the rhizosphere fungal communities from continuously grown OSR were significantly different to those from other rotations. This was due primarily to an increase in abundance of two fungi which showed 100% and 95% DNA identity to the plant pathogens Olpidium brassicae and Pyrenochaeta lycopersici, respectively. Real-time PCR confirmed that there was significantly more of these fungi in the continuously grown OSR than the other rotations. These two fungi were isolated from the field and used to inoculate OSR and Brassica oleracea grown under controlled conditions in a glasshouse to determine their effect on yield. At high doses, Olpidium brassicae reduced top growth and root biomass in seedlings and reduced branching and subsequent pod and seed production. Pyrenochaeta sp. formed lesions on the roots of seedlings, and at high doses delayed flowering and had a negative impact on seed quantity and quality