TY - JOUR AB - Partner specificity is a well-documented phenomenon in biotic interactions, yet the factors that determine specificity in plant-fungal associations remain largely unknown. By utilizing composite soil samples, we identified the predictors that drive partner specificity in both plants and fungi, with a particular focus on ectomycorrhizal associations. Fungal guilds exhibited significant differences in overall partner preference and avoidance, richness, and specificity to specific tree genera. The highest level of specificity was observed in root endophytic and ectomycorrhizal associations, while the lowest was found in arbuscular mycorrhizal associations. The majority of ectomycorrhizal fungal species showed a preference for one of their partner trees, primarily at the plant genus level. Specialist ectomycorrhizal fungi were dominant in belowground communities in terms of species richness and relative abundance. Moreover, all tree genera (and occasionally species) demonstrated a preference for certain fungal groups. Partner specificity was not related to the rarity of fungi or plants or environmental conditions, except for soil pH. Depending on the partner tree genus, specific fungi became more prevalent and relatively more abundant with increasing stand age, tree dominance, and soil pH conditions optimal for the partner tree genus. The richness of partner tree species and increased evenness of ectomycorrhizal fungi in multi-host communities enhanced the species richness of ectomycorrhizal fungi. However, it was primarily the partner-generalist fungi that contributed to the high diversity of ectomycorrhizal fungi in mixed forests. AU - Tedersoo, L.* AU - Drenkhan, R.* AU - Abarenkov, K.* AU - Anslan, S.* AU - Bahram, M.* AU - Bitenieks, K.* AU - Buegger, F. AU - Gohar, D.* AU - Hagh-Doust, N.* AU - Klavina, D.* AU - Makovskis, K.* AU - Zusevica, A.* AU - Pritsch, K. AU - Padari, A.* AU - Polme, S.* AU - Rahimlou, S.* AU - Rungis, D.* AU - Mikryukov, V.* C1 - 70433 C2 - 55619 CY - 111 River St, Hoboken 07030-5774, Nj Usa TI - The influence of tree genus, phylogeny, and richness on the specificity, rarity, and diversity of ectomycorrhizal fungi. JO - Environ. Microbiol. Rep. VL - 16 IS - 2 PB - Wiley PY - 2024 SN - 1758-2229 ER - TY - JOUR AB - Phosphorus is one of the most important macronutrient for plants. In agriculture, amending fertilizer with phosphorus (P) is common practice. However, natural phosphorus sources are finite, making research for more sustainable management practices necessary. We postulated that the addition of carbon (C) and nitrogen (N) would stimulate phosphorus mobilization by bacteria because of their desire to maintain a stable intracellular C:N:P stoichiometry. Therefore, we chose a metagenomic approach to investigate two agricultural soils, which only received mineral N fertilizer or mineral N and organic fertilizer for more than 20 years. The most abundant genes involved in the acquisition of external P sources in our study were those involved in solubilization and subsequent uptake of inorganic phosphorus. Independent of site and season, the relative abundance of genes involved in P turnover was not significantly affected by the addition of fertilizers. However, the type of fertilization had a significant impact on the diversity pattern of bacterial families harbouring genes coding for the different P transformation processes. This gives rise to the possibility that fertilizers can substantially change phosphorus turnover efficiency by favouring different families. Additionally, none of the families involved in phosphorus turnover covered all investigated processes. Therefore, promoting bacteria which play an essential role specifically in mobilization of hardly accessible phosphorus could help to secure the phosphorus supply of plants in soils with low P input. AU - Grafe, M. AU - Goers, M.* AU - Tucher, S.V.* AU - Baum, C.* AU - Zimmer, D.* AU - Leinweber, P.* AU - Vestergaard, G. AU - Kublik, S. AU - Schloter, M. AU - Schulz, S. C1 - 53447 C2 - 44793 SP - 320-327 TI - Bacterial potentials for uptake, solubilization and mineralization of extracellular phosphorus in agricultural soils are highly stable under different fertilization regimes. JO - Environ. Microbiol. Rep. VL - 10 IS - 3 PY - 2018 SN - 1758-2229 ER - TY - JOUR AU - Dixon, R.* AU - Hartmann, A. C1 - 50683 C2 - 42828 SP - 179-181 TI - Novel insights into ecological distribution and plant growth promotion by nitrogen-fixing endophytes - how specialised are they? JO - Environ. Microbiol. Rep. VL - 9 IS - 3 PY - 2017 SN - 1758-2229 ER - TY - JOUR AB - Root exudates shape microbial communities at the plant soil interface. Here we compared bacterial communities that utilise plant-derived carbon in the rhizosphere of wheat in different soil depths, including topsoil, as well as two subsoil layers up to 1 m depth. The experiment was performed in a green house using soil monoliths with intact soil structure taken from an agricultural field. To identify bacteria utilizing plant derived carbon, (13) C-CO2 labelling of plants was performed for two weeks at the EC50 stage, followed by stable isotope probing of extracted DNA from the rhizosphere combined with 16S rRNA gene-based amplicon sequencing. Our findings suggest substantially different bacterial key players and interaction mechanisms between plants and bacteria utilising plant-derived carbon in the rhizosphere of subsoils and topsoil. Among the three soil depths, clear differences were found in (13) C enrichment pattern across abundant operational taxonomic units (OTUs). Whereas OTUs linked to Proteobacteria were enriched in (13) C mainly in the topsoil, in both subsoil layers OTUs related to Cohnella, Paenibacillus, Flavobacterium showed a clear (13) C signal, indicating an important, so far overseen role of Firmicutes and Bacteriodetes in the subsoil rhizosphere. AU - Uksa, M. AU - Buegger, F. AU - Gschwendtner, S. AU - Lueders, T. AU - Kublik, S. AU - Kautz, T.* AU - Athmann, M.* AU - Köpke, U.* AU - Charles Munch, J.* AU - Schloter, M. AU - Fischer, D. C1 - 51851 C2 - 43424 CY - Hoboken SP - 729-741 TI - Bacteria utilising plant-derived carbon in the rhizosphere of Triticum aestivum change in different depths of an arable soil. JO - Environ. Microbiol. Rep. VL - 9 IS - 6 PB - Wiley PY - 2017 SN - 1758-2229 ER - TY - JOUR AB - The trophic interactions between viruses, bacteria and protists play a crucial role in structuring microbial communities and regulating nutrient and organic matter flux. Here, we show that the impact on viral density by heterotrophic flagellates is related to their feeding behaviour (feeding on sedimented particles – Thaumatomonas coloniensis, filter feeding of suspended particles – Salpingoeca sp., and actively searching raptorial feeding – Goniomonas truncata). Phage MS2 was co-incubated with flagellates and the natural bacterial and viral community originating from the same groundwater habitats where the flagellates were isolated. Three complementary assays, i.e. flow cytometry, qPCR and plaque assay, were used for enumeration of total viruses, total MS2 phages, and free and infectious MS2, respectively, to provide insights into the grazing mechanisms of the flagellates on viruses. Phage MS2 was actively removed by the suspension feeders T. coloniensis and Salpingoeca sp. in contrast with the actively raptoriale grazer G. truncata. The decline of viral titre was demonstrated to be caused by ingestion rather than random absorption by both qPCR and locating protein fluorescently labelled MS2 inside the flagellates. Further, we indicate that phages can be used as a minor carbon source for flagellates. Collectively, these data demonstrate that eliminating viruses can be an important function of protists in microbial food webs, carbon cycling and potentially water quality control. AU - Deng, L. AU - Krauss, S. AU - Feichtmayer, J. AU - Hofmann, R. AU - Arndt, H.* AU - Griebler, C. C1 - 31043 C2 - 34116 CY - Hoboken SP - 325-330 TI - Grazing of heterotrophic flagellates on viruses is driven by feeding behaviour. JO - Environ. Microbiol. Rep. VL - 6 IS - 4 PB - Wiley-blackwell PY - 2014 SN - 1758-2229 ER - TY - JOUR AB - Brazilian sugarcane has been shown to obtain part of its nitrogen via biological nitrogen fixation (BNF). Recent reports, based on the culture independent sequencing of bacterial nifH complementary DNA (cDNA) from sugarcane tissues, have suggested that members of the Bradyrhizobium genus could play a role in sugarcane-associated BNF. Here we report on the isolation of Bradyrhizobium spp. isolates and a few other species from roots of sugarcane cultivar RB867515 by two cultivation strategies: direct isolation on culture media and capture of Bradyrhizobium spp. using the promiscuous legume Vigna unguiculata as trap-plant. Both strategies permitted the isolation of genetically diverse Bradyrhizobium spp. isolates, as concluded from enterobacterial repetitive intergenic consensus polymerase chain reaction (PCR) fingerprinting and 16S ribosomal RNA, nifH and nodC sequence analyses. Several isolates presented nifH phylotypes highly similar to nifH cDNA phylotypes detected in field-grown sugarcane by a culture-independent approach. Four isolates obtained by direct plate cultivation were unable to nodulate V. unguiculata and, based on PCR analysis, lacked a nodC gene homologue. Acetylene reduction assay showed in vitro nitrogenase activity for some Bradyrhizobium spp. isolates, suggesting that these bacteria do not require a nodule environment for BNF. Therefore, this study brings further evidence that Bradyrhizobium spp. may play a role in sugarcane-associated BNF under field conditions. AU - Rouws, L.* AU - Leite, J.* AU - Feitosa de Matos, G.* AU - Zilli, J.E.* AU - Coelho, M.R.* AU - Xavier, G.R.* AU - Fischer, D. AU - Hartmann, A. AU - Reis, V.M.* AU - Baldani, J.I.* C1 - 28729 C2 - 33528 CY - Hoboken SP - 354-363 TI - Endophytic Bradyrhizobium spp. isolates from sugarcane obtained through different culture strategies. JO - Environ. Microbiol. Rep. VL - 6 IS - 4 PB - Wiley-Blackwell PY - 2014 SN - 1758-2229 ER - TY - JOUR AB - Hydrocarbon contaminants in groundwater can be degraded by microbes under different redox settings, forming hot spots of degradation especially at the fringes of contaminant plumes. At a tar-oil-contaminated aquifer in Germany, it was previously shown that the distribution of anaerobic toluene degraders as traced via catabolic and ribosomal marker genes is highly correlated to zones of increased anaerobic degradation at the lower fringe of the plume. Here, we trace the respective distribution of aerobic toluene degraders over a fine-scale depth transect of sediments taken at the upper fringe of the plume and below, based on the analysis of 16S rRNA genes as well as catabolic markers in intervals of 310cm. Well-defined small-scale distribution maxima of typical aerobic degrader lineages within the Pseudomonadaceae, Comamonadaceae and Burkholderiaceae are revealed over the redox gradient. An unexpected maximal abundance of 9.2x106 toluene monooxygenase (tmoA) genes per g of sediment was detected in the strongly reduced plume core, and gene counts did not increase towards the more oxidized upper plume fringe. This may point towards unusual ecological controls of these yet unidentified aerobic degraders, and indicates that competitive niche partitioning between aerobic and anaerobic hydrocarbon degraders in the field is not yet fully understood. These findings demonstrate the potential of catabolic marker gene assays in elaborating the ecology of contaminant plumes, which is a prerequisite for developing integrated monitoring strategies for natural attenuation. AU - Larentis, M. AU - Hoermann, K. AU - Lueders, T. C1 - 23634 C2 - 31272 SP - 225-234 TI - Fine-scale degrader community profiling over an aerobic/anaerobic redox gradient in a toluene-contaminated aquifer. JO - Environ. Microbiol. Rep. VL - 5 IS - 2 PB - Wiley-Blackwell PY - 2013 SN - 1758-2229 ER -