Browsing by Subject "MICROBIAL COMMUNITY"

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  • Sun, Hui; Santalahti, Minna; Pumpanen, Jukka; Köster, Kajar; Berninger, Frank; Raffaello, Tommaso; Asiegbu, Fred O.; Heinonsalo, Jussi (2016)
    Soil microbial responses to fire are likely to change over the course of forest recovery. Investigations on long-term changes in bacterial dynamics following fire are rare. We characterized the soil bacterial communities across three different times post fire in a 2 to 152-year fire chronosequence by Illumina MiSeq sequencing, coupled with a functional gene array (GeoChip). The results showed that the bacterial diversity did not differ between the recently and older burned areas, suggesting a concomitant recovery in the bacterial diversity after fire. The differences in bacterial communities over time were mainly driven by the rare operational taxonomic units (OTUs <0.1%). Proteobacteria (39%), Acidobacteria (34%) and Actinobacteria (17%) were the most abundant phyla across all sites. Genes involved in C and N cycling pathways were present in all sites showing high redundancy in the gene profiles. However, hierarchical cluster analysis using gene signal intensity revealed that the sites with different fire histories formed separate clusters, suggesting potential differences in maintaining essential biogeochemical soil processes. Soil temperature, pH and water contents were the most important factors in shaping the bacterial community structures and function. This study provides functional insight on the impact of fire disturbance on soil bacterial community.
  • Partanen, Pasi; Hultman, Jenni; Paulin, Lars; Auvinen, Petri; Romantschuk, Martin (2010)
  • Li, Quan; Song, Xinzhang; Yrjälä, Kim; Lv, Jianhua; Li, Yongfu; Wu, Jiasheng; Qin, Hua (2020)
    Increased reactive N deposition has widespread effects on terrestrial ecosystems, such as biodiversity loss, soil acidification, as well as stimulated plant growth. Empirical studies show that biochar often affects soil quality, crop productivity, soil microbial community composition and enzyme activities. However, the effect of biochar addition on forest soil bacterial community along with enzyme activities under nitrogen (N) deposition and its related mechanisms have not been well studied yet. Therefore, a 2-year field study was conducted to investigate the effects of biochar amendment (0, 20, 40 kg biochar ha−1 yr−1) on soil nutrients, enzyme activities, and bacterial community in a Torreya grandis orchard under different levels of N deposition (0, 30, 60 kg N ha−1 yr−1). N deposition significantly increased soil nutrients availability, such as N, phosphorus (P) and potassium (K), while biochar amendment led to significant increase in soil pH, organic carbon (SOC), total N (TN), total P (TP), available P (AP) and available K (AK). Both N deposition and biochar amendment significantly decreased the soil microbial biomass carbon (MBC), altered soil microbial community and enzyme activities significantly. Biochar addition increased the relative abundance of phylum Proteobacteria under different levels of N deposition, but had variable effect on Acidobacteria groups. Non-metric multidimensional scaling (NMDS) indicated that biochar amendment can mitigate the effect of N deposition on soil bacterial community composition and enzyme activities. Soil pH and SOC played an important role in shaping soil bacterial community composition, while available AP and AK contents significantly related to the variation of soil enzyme activities. Structure equation modeling (SEM) revealed that N deposition had negative effect on soil enzyme activities while biochar amendment can mitigate this negative effect through increasing AP content. Our result suggests that biochar amendment can mitigate the alteration of soil bacterial community and enzyme activities induced by N deposition, and this mitigation effect was linked to the alteration of soil physicochemical properties, especially the increased AP content. Thus, biochar amendment could be a promising way to develop sustainable forest management under increasing N deposition.
  • Xia, Zhichao; Yu, Lei; He, Yue; Korpelainen, Helena; Li, Chunyang (2019)
    Tree performance in mixed-species forest plantations is ultimately the net result of positive and negative interactions among species. Despite increasing knowledge of interspecific interactions, relatively little is known about the chemical mechanisms mediating such interactions. We constructed mixed planting systems with two species including Chinese fir (Cunninghamia lanceolata (Lamb.) Hook) and broadleaf species Cinnamomum camphora L. Presl, Elaeocarpus decipiens Hemsl, Liquidambar formosana Hance, or Michelia macclurei Dandy. Based on a series of manipulative experiments, we investigated the performance of Chinese fir and analyzed root placement patterns and the composition of main soil microbial groups. The broadleaf trees influenced the growth of Chinese fir roots more than the growth of shoots. Furthermore, C. camphora roots released allelochemicals into the soil environment, resulting in growth inhibition of Chinese fir and changes in main soil microbial groups. However, when grown with E. decipiens and M. macclurei, the growth of Chinese fir was consistently promoted. It responded by enhancing its root growth and altering root behavior, resulting in a shift from growth inhibition to chemical facilitation. These positive inter-specific interactions also stimulated changes in the composition of soil microbes. Complementary experiments indicated that non-toxic signaling molecules in the root exudates of E. decipiens and M. macclurei may be responsible for mediating positive root-root interactions and regulating the composition of main soil microbial groups. Thus, our study demonstrated that broadleaf species chemically mediate the growth of Chinese fir through root exudates. Such a novel mechanism offers many implications and applications for reforestation programs undertaken to rehabilitate forest plantations that suffer from declining productivity related to densely planted monocultures.
  • Dong, Lili; Sun, Tao; Berg, Björn; Zhang, Lili; Zhang, Quanquan (2019)
    Despite the importance of decomposition for biogeochemical cycles, it is still not clear how this process is affected by different forms of nitrogen (N). Equal amounts of N with different ratios of inorganic N : organic N (0 : 0, 10 : 0, 7 : 3, 5 : 5, 3 : 7, and 0 : 10) were added to the soil in a steppe. We studied the response of litter decomposition to different forms of N enrichment. The treatment with 30% organic N resulted in the fastest decomposition, which was higher than with inorganic N or organic N addition alone. Our results highlight the need for studies of N deposition on carbon cycles that consider different components in N deposition.
  • Saarenheimo, Jatta; Rissanen, Antti J.; Arvola, Lauri; Nykänen, Hannu; Lehmann, Moritz F.; Tiirola, Marja (2015)
    We studied potential links between environmental factors, nitrous oxide (N2O) accumulation, and genetic indicators of nitrite and N2O reducing bacteria in 12 boreal lakes. Denitrifying bacteria were investigated by quantifying genes encoding nitrite and N2O reductases (nirS/nirK and nosZ, respectively, including the two phylogenetically distinct clades nosZ(I) and nosZ(II)) in lake sediments. Summertime N2O accumulation and hypolimnetic nitrate concentrations were positively correlated both at the inter-lake scale and within a depth transect of an individual lake (Lake Vanajavesi). The variability in the individual nirS, nirK, nosZ(I), and nosZ(II) gene abundances was high (up to tenfold) among the lakes, which allowed us to study the expected links between the ecosystem's nir-vs-nos gene inventories and N2O accumulation. Inter-lake variation in N2O accumulation was indeed connected to the relative abundance of nitrite versus N2O reductase genes, i.e. the (nirS+nirK)/nosZ(I) gene ratio. In addition, the ratios of (nirS+ nirK)/nosZ(I) at the inter-lake scale and (nirS+ nirK)/nosZ(I+II) within Lake Vanajavesi correlated positively with nitrate availability. The results suggest that ambient nitrate concentration can be an important modulator of the N2O accumulation in lake ecosystems, either directly by increasing the overall rate of denitrification or indirectly by controlling the balance of nitrite versus N2O reductase carrying organisms.
  • Pessi, Igor S.; Viitamäki, Sirja; Virkkala, Anna-Maria; Eronen-Rasimus, Eeva; Delmont, Tom O.; Marushchak, Maija E.; Luoto, Miska; Hultman, Jenni (2022)
    Background In contrast to earlier assumptions, there is now mounting evidence for the role of tundra soils as important sources of the greenhouse gas nitrous oxide (N2O). However, the microorganisms involved in the cycling of N2O in this system remain largely uncharacterized. Since tundra soils are variable sources and sinks of N2O, we aimed at investigating differences in community structure across different soil ecosystems in the tundra. Results We analysed 1.4 Tb of metagenomic data from soils in northern Finland covering a range of ecosystems from dry upland soils to water-logged fens and obtained 796 manually binned and curated metagenome-assembled genomes (MAGs). We then searched for MAGs harbouring genes involved in denitrification, an important process driving N2O emissions. Communities of potential denitrifiers were dominated by microorganisms with truncated denitrification pathways (i.e., lacking one or more denitrification genes) and differed across soil ecosystems. Upland soils showed a strong N2O sink potential and were dominated by members of the Alphaproteobacteria such as Bradyrhizobium and Reyranella. Fens, which had in general net-zero N2O fluxes, had a high abundance of poorly characterized taxa affiliated with the Chloroflexota lineage Ellin6529 and the Acidobacteriota subdivision Gp23. Conclusions By coupling an in-depth characterization of microbial communities with in situ measurements of N2O fluxes, our results suggest that the observed spatial patterns of N2O fluxes in the tundra are related to differences in the composition of denitrifier communities.
  • Sinkko, Hanna; Hepolehto, Iina; Lyra, Christina; Rinta-Kanto, Johanna M.; Villnäs, Anna; Norkko, Joanna; Norkko, Alf; Timonen, Sari (2019)
    Coastal hypoxia is a major environmental problem worldwide. Hypoxia-induced changes in sediment bacterial communities harm marine ecosystems and alter biogeochemical cycles. Nevertheless, the resistance of sediment bacterial communities to hypoxic stress is unknown. We investigated changes in bacterial communities during hypoxic-anoxic disturbance by artificially inducing oxygen deficiency to the seafloor for 0, 3, 7, and 48 days, with subsequent molecular biological analyses. We further investigated relationships between bacterial communities, benthic macrofauna and nutrient effluxes across the sediment-water-interface during hypoxic-anoxic stress, considering differentially abundant operational taxonomic units (OTUs). The composition of the moderately abundant OTUs changed significantly after seven days of oxygen deficiency, while the abundant and rare OTUs first changed after 48 days. High bacterial diversity maintained the resistance of the communities during oxygen deficiency until it dropped after 48 days, likely due to anoxia-induced loss of macrofaunal diversity and bioturbation. Nutrient fluxes, especially ammonium, correlated positively with the moderate and rare OTUs, including potential sulfate reducers. Correlations may reflect bacteria-mediated nutrient effluxes that accelerate eutrophication. The study suggests that even slightly higher bottom-water oxygen concentrations, which could sustain macrofaunal bioturbation, enable bacterial communities to resist large compositional changes and decrease the harmful consequences of hypoxia in marine ecosystems.
  • Marushchak, M. E.; Friborg, T.; Biasi, C.; Herbst, M.; Johansson, T.; Kiepe, I.; Liimatainen, M.; Lind, S. E.; Martikainen, P. J.; Virtanen, Tarmo; Soegaard, H.; Shurpali, N. J. (2016)
    Methane (CH4) fluxes were investigated in a subarctic Russian tundra site in a multi-approach study combining plot-scale data, ecosystem-scale eddy covariance (EC) measurements, and a fine-resolution land cover classification scheme for regional upscaling. The flux data as measured by the two independent techniques resulted in a seasonal (May-October 2008) cumulative CH4 emission of 2.4 (EC) and 3.7 gCH(4) m(-2) (manual chambers) for the source area representative of the footprint of the EC instruments. Upon upscaling for the entire study region of 98.6 km(2), the chamber measured flux data yielded a regional flux estimate of 6.7 gCH(4) m(-2) yr(-1). Our upscaling efforts accounted for the large spatial variability in the distribution of the various land cover types (LCTs) predominant at our study site. Wetlands with emissions ranging from 34 to 53 gCH(4) m(-2) yr(-1) were the most dominant CH4-emitting surfaces. Emissions from thermokarst lakes were an order of magnitude lower, while the rest of the landscape (mineral tundra) was a weak sink for atmospheric methane. Vascular plant cover was a key factor in explaining the spatial variability of CH4 emissions among wetland types, as indicated by the positive correlation of emissions with the leaf area index (LAI). As elucidated through a stable isotope analysis, the dominant CH4 release pathway from wetlands to the atmosphere was plant-mediated diffusion through aerenchyma, a process that discriminates against C-13-CH4. The CH4 released to the atmosphere was lighter than that in the surface porewater, and delta C-13 in the emitted CH4 correlated negatively with the vascular plant cover (LAI). The mean value of delta C-13 obtained here for the emitted CH4, 68.2 +/- 2.0 %, is within the range of values from other wetlands, thus reinforcing the use of inverse modelling tools to better constrain the CH4 budget. Based on the IPCC A1B emission scenario, a temperature increase of 6.1 degrees C relative to the present day has been predicted for the European Russian tundra by the end of the 21st Century. A regional warming of this magnitude will have profound effects on the permafrost distribution leading to considerable changes in the regional landscape with a potential for an increase in the areal extent of CH4-emitting wet surfaces.
  • Pitkäranta, Miia Johanna; Meklin, Teija; Hyvarinen, Anne; Nevalainen, Aino; Paulin, Lars; Auvinen, Petri; Lignell, Ulla; Rintala, Helena (2011)
  • Janket, Sok-Ja; Benwait, Jaspreet; Isaac, Paul; Ackerson, Leland K.; Meurman, Jukka H. (2019)
    Recent results of randomized trials testing the efficacy of xylitol in caries prevention have been conflicting. This narrative review reveals the sources of discrepancy. The following databases were searched for the terms xylitol or artificial sweeteners restricted to the English language: PubMed, Web of Science, Evidenced-Based Medicine, Scopus, and the Cochrane database. In a separate search, the terms dental caries or cariogenicity or glucosyltransferase or low glycemic or low insulinemic or dysbiosis or gut microbiome were used and then combined. In section I, findings regarding the role of xylitol in dental caries prevention, the appropriateness of research methods, and the causes for potential biases are summarized. In section II, the systemic effects of xylitol on gut microbiota as well as low-glycemic/insulinogenic systemic effects are evaluated and summarized. The substitution of a carbonyl group with an alcohol radical in xylitol hinders its absorption and slowly releases sugar into the bloodstream. This quality of xylitol is beneficial for diabetic patients to maintain a constant glucose level. Although this quality of xylitol has been proven in in vitro and animal studies, it has yet to be proven in humans. Paradoxically, recent animal studies reported hyperglycemia and intestinal dysbiosis with artificial sweetener consumption. Upon careful inspection of evidence, it was revealed that these reports may be due to misinterpretation of original references or flaws in study methodology. Any systemic benefits of xylitol intake must be weighed in consideration with the well-established adverse gastrointestinal consequences. The contribution of xylitol to gut dysbiosis that may affect systemic immunity warrants further research.
  • Guo, Qingxue; Yan, Lijuan; Korpelainen, Helena; Niinemets, Ülo; Li, Chunyang (2019)
    The impact of conspecific and heterospecific neighboring plants on soil bacterial and fungal communities has never been explored in a forest ecosystem. In the present study, we first investigated soil microbial communities in three plantations: Larix kaempferi monoculture, L. olgensis monoculture and their mixture. Then, a two-year growth experiment was conducted to investigate the effects of intra- and inter-specific interactions of L. kaempferi and L. olgensis on rhizosphere microbial communities at two different nitrogen levels. The results demonstrated clear differences in the beta-diversity and composition of bacteria and fungi among the three plantations, which implied the presence of different effects of plant-plant interactions on soil microbial communities. The results of the pot experiment showed that L. kaempferi suffered from greater neighbor effects from its conspecific neighbor regardless of N fertilization, although the effect declined when L. kaempferi was grown with L. olgensis under N fertilization. Changes in intra- and inter-specific plant interactions significantly impacted the chemical and biological properties of soil under N fertilization, with lower concentrations of NH4+, and lower soil microbial biomass (C-Mic) and soil carbon nitrogen biomass (N-Mic) under intra-specific plant interactions of L. kaempferi (KK) compared to inter-specific interactions of L. kaempferi and L. olgensis (KO). N fertilization increased bacterial and fungal alpha diversities in the rhizosphere soil of KO. For the beta diversity, the PERMANOVA results demonstrated that there was a significant impact of intra- and inter-specific plant interactions on soil microbial communities, with KK significantly differing from intra-specific plant interactions of L. olgensis (OO) and KO. The two plant species and N fertilization showed specific effects on the soil microbial composition, particularly on the fungal community. Both L. olgensis and N fertilization increased the abundance of Ascomycota but reduced that of Basidiomycota, and even shifted the dominance from Basidiomycota to Ascomycota under KO combined with N fertilization.
  • Xia, Zhichao; He, Yue; Yu, Lei; Li, Zhijun; Korpelainen, Helena; Li, Chunyang (2021)
    How the root metabolic profiles and rhizosphere bacterial communities of dioecious plants respond to soil properties and sex identity is largely unknown. In this study, we analyzed root phenolic metabolomes and rhizosphere bacterial microbiomes of Populus euphratica females and males in two P. euphratica plantations with different soil properties to reveal the relative importance of soil and sex effects, and to decipher associations of certain phenolic compounds with specific bacterial taxa. We found that the relative abundances of bacterial OTUs and phenolic metabolites were closely linked to soil properties and sex identity. Soil is the main filter influencing the root phenolic metabolic profiles and rhizosphere bacterial communities of P. euphratica, while sexes and their interactions with soil properties are secondary factors. Differences in the diversity and evenness of phenolic metabolites were affected by plant sex, but not by soil properties. Conversely, the diversity and evenness of bacterial communities were affected by soil properties independent of plant sex. A multiple regression model indicated the presence of associations between root phenolic metabolites and specific soil bacteria taxa. Furthermore, all bacterial phyla and families correlated with at least one phenolic metabolite. Especially, both Nitrosomonadaceae and Cytophagaceae positively correlated with salicylic acid. Thus, our study provides new insights into the ecological mechanism that maintains rhizosphere bacterial communities in P. euphratica plantations in the desert area.
  • Anasonye, Festus; Tammeorg, Priit; Parshintsev, Evgeny; Riekkola, Marja-Liisa; Tuomela, Marja Tuulikki (2018)
    The use of biochar (BC) has been suggested for remediation of contaminated soils. This study aims to investigate the role of microorganisms in sorption of PAH to BC-amended soils. Fungi, especially the wood and litter-degrading fungi, have shown the ability for humification and to degrade recalcitrant molecules, and are thus suitable model organisms. Haplic Arenosol with high organic matter content was chosen to highlight the importance of soil organic matter (SOM) in PAH sorption, possibly to form non-extractable residue. Basidiomycetous fungi Agrocybe praecox and Phanerochaete velutina grown on pine bark were inoculated in organic matter (OM)-rich Haplic Arenosol and OM-poor sandy loam with either BC or chemically activated BC (ABC) and 14C-labelled pyrene for 60 days. Fungi did not mineralize pyrene, but increased sorption up to 47–56% in BC-amended Haplic Arenosol in comparison with controls (13–25%) without a fungus irrespective of the presence of an adsorbent. In OM-poor sandy loam, only 9–12% of pyrene was sorbed to amended soil in the presence of fungus and adsorbent. The results suggest that BC and fungal amendment increased sorption of pyrene, especially to Haplic Arenosol more than by either BC or fungi alone.
  • Francini, G.; Hui, N.; Jumpponen, A.; Kotze, D. J.; Romantschuk, M.; Allen, J. A.; Setala, H. (2018)
    Plant functional type influences the abundance and distribution of soil biota. With time, as root systems develop, such effects become more apparent. The relationship of plant type and time with the structure and abundance of soil microbial and invertebrate communities has been widely investigated in a variety of systems. However, much less is known about long-term soil community dynamics within the context of urban environments. In this study, we investigated how soil microbes, nematodes and earthworms respond to different plant functional types (lawns only and lawns with deciduous or evergreen trees) and park age in 41 urban parks in southern Finland. As non-urban controls we included deciduous and evergreen trees in 5 forest sites. We expected that microbial biomass and the relative abundance of fungi over bacteria would increase with time. We also expected major differences in soil microbial and nematode communities depending on vegetation: we hypothesized that i) the presence of trees, and evergreens in particular, would support a greater abundance of fungi and fungal-feeding nematodes over bacteria and bacterial-feeding nematodes and ii) the fungi to bacteria ratio would be lowest in lawns, with deciduous trees showing intermediate values. In contrast to our predictions, we showed that old deciduous trees, rather than evergreens, supported the highest fungal abundances and fungal-feeding nematodes in the soil. Consistent with our predictions, microbial biomass in urban park soils tended to increase with time, whereas - in contrast to our hypotheses - fungal-feeding nematode abundance declined. Even in the oldest parks included in the current study, microbial biomass estimates never approximated those in the minimally managed natural forests, where biomass estimates were three times higher. Anecic earthworm abundance also increased with time in urban parks, whereas abundances of fungal-feeding, plant-feeding and omnivorous nematodes, as well as those of epigeic and endogeic earthworms remained constant with time and without any distinct differences between urban parks and the control forests. Our findings highlight that although urban park soils harbor diverse soil communities and considerable microbial biomass, they are distinct from adjacent natural sites in community composition and biomass.