Browsing by Subject "MICROBIAL COMMUNITIES"

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  • Ma, Yang; Qu, Zhao-Lei; Liu, Bing; Tan, Jia-Jin; Asiegbu, Fred O.; Sun, Hui (2020)
    Pine wilt disease (PWD) caused by the nematode Bursaphelenchus xylophilus is a devastating disease in conifer forests in Eurasia. However, information on the effect of PWD on the host microbial community is limited. In this study, the bacterial community structure and potential function in the needles, roots, and soil of diseased pine were studied under field conditions using Illumina MiSeq coupled with Phylogenetic Investigation of Communities by Reconstruction of Unobserved states (PICRUSt) software. The results showed that the community and functional structure of healthy and diseased trees differed only in the roots and needles, respectively (p <0.05). The needles, roots, and soil formed unique bacterial community and functional structures. The abundant phyla across all samples were Proteobacteria (41.9% of total sequence), Actinobacteria (29.0%), Acidobacteria (12.2%), Bacteroidetes (4.8%), and Planctomycetes (2.1%). The bacterial community in the healthy roots was dominated by Acidobacteria, Planctomycetes, and Rhizobiales, whereas in the diseased roots, Proteobacteria, Firmicutes, and Burkholderiales were dominant. Functionally, groups involved in the cell process and genetic information processing had a higher abundance in the diseased needles, which contributed to the difference in functional structure. The results indicate that PWD can only affect the host bacteria community structure and function in certain anatomical regions of the host tree.
  • Tiwari, Ananda; Hokajärvi, Anna-Maria; Santo Domingo, Jorge; Elk, Michael; Jayaprakash, Balamuralikrishna; Ryu, Hodon; Siponen, Sallamaari; Vepsäläinen, Asko; Kauppinen, Ari; Puurunen, Osmo; Artimo, Aki; Perkola, Noora; Huttula, Timo; Miettinen, Ilkka T.; Pitkänen, Tarja (2021)
    Background Rivers and lakes are used for multiple purposes such as for drinking water (DW) production, recreation, and as recipients of wastewater from various sources. The deterioration of surface water quality with wastewater is well-known, but less is known about the bacterial community dynamics in the affected surface waters. Understanding the bacterial community characteristics -from the source of contamination, through the watershed to the DW production process-may help safeguard human health and the environment. Results The spatial and seasonal dynamics of bacterial communities, their predicted functions, and potential health-related bacterial (PHRB) reads within the Kokemaenjoki River watershed in southwest Finland were analyzed with the 16S rRNA-gene amplicon sequencing method. Water samples were collected from various sampling points of the watershed, from its major pollution sources (sewage influent and effluent, industrial effluent, mine runoff) and different stages of the DW treatment process (pre-treatment, groundwater observation well, DW production well) by using the river water as raw water with an artificial groundwater recharge (AGR). The beta-diversity analysis revealed that bacterial communities were highly varied among sample groups (R = 0.92, p <0.001, ANOSIM). The species richness and evenness indices were highest in surface water (Chao1; 920 +/- 10) among sample groups and gradually decreased during the DW treatment process (DW production well; Chao1: 320 +/- 20). Although the phylum Proteobacteria was omnipresent, its relative abundance was higher in sewage and industrial effluents (66-80%) than in surface water (55%). Phyla Firmicutes and Fusobacteria were only detected in sewage samples. Actinobacteria was more abundant in the surface water (>= 13%) than in other groups (= 13%) than in others (
  • Yan, Lijuan; Sinkko, Hanna; Penttinen, Petri; Lindström, Kristina (2016)
    The widespread use of motor oil makes it a notable risk factor to cause scattered contamination in soil. The monitoring of microbial community dynamics can serve as a comprehensive tool to assess the ecological impact of contaminants and their disappearance in the ecosystem. Hence, a field study was conducted to monitor the ecological impact of used motor oil under different perennial cropping systems (fodder galega, brome grass, galega-brome grass mixture and bare fallow) in a boreal climate zone. Length heterogeneity PCR characterized a successional pattern in bacterial community following oil contamination over a four-year bioremediation period. Soil pH and electrical conductivity were associated with the shifts in bacterial community composition. Crops had no detectable effect on bacterial community composition or complexity. However, the legume fodder galega increased soil microbial biomass, expressed as soil total DNA. Oil contamination induced an abrupt change in bacterial community composition at the early stage, yet the effect did not last as long as the oil in soil. The successional variation in bacterial community composition can serve as a sensitive ecological indicator of oil contamination and remediation in situ. (C) 2015 Elsevier B.V. All rights reserved.
  • Pershina, Elizaveta; Valkonen, Jari Pekka Tapani; Kurki, Paivi; Ivanova, Ekaterina; Chirak, Evgeny; Korvigo, Ilia; Provorov, Nykolay; Andronov, Evgeny (2015)
    One of the most important challenges in agriculture is to determine the effectiveness and environmental impact of certain farming practices. The aim of present study was to determine and compare the taxonomic composition of the microbiomes established in soil following long-term exposure (14 years) to a conventional and organic farming systems (CFS and OFS accordingly). Soil from unclared forest next to the fields was used as a control. The analysis was based on RT-PCR and pyrosequencing of 16S rRNA genes of bacteria and archaea. The number of bacteria was significantly lower in CFS than in OFS and woodland. The highest amount of archaea was detected in woodland, whereas the amounts in CFS and OFS were lower and similar. The most common phyla in the soil microbial communities analyzed were Proteobacteria (57.9%), Acidobacteria (16.1%), Actinobacteria (7.9%), Verrucomicrobia (2.0%), Bacteroidetes (2.7%) and Firmicutes (4.8%). Woodland soil differed from croplands in the taxonomic composition of microbial phyla. Croplands were enriched with Proteobacteria (mainly the genus Pseudomonas), while Acidobacteria were detected almost exclusively in woodland soil. The most pronounced differences between the CFS and OFS microbiomes were found within the genus Pseudomonas, which significantly (p<0,05) increased its number in CFS soil compared to OFS. Other differences in microbiomes of cropping systems concerned minor taxa. A higher relative abundance of bacteria belonging to the families Oxalobacteriaceae, Koribacteriaceae, Nakamurellaceae and genera Ralstonia, Paenibacillus and Pedobacter was found in CFS as compared with OFS. On the other hand, microbiomes of OFS were enriched with proteobacteria of the family Comamonadaceae (genera Hylemonella) and Hyphomicrobiaceae, actinobacteria from the family Micrococcaceae, and bacteria of the genera Geobacter, Methylotenera, Rhizobium (mainly Rhizobium leguminosarum) and Clostridium. Thus, the fields under OFS and CFS did not differ greatly for the composition of the microbiome. These results, which were also confirmed by cluster analysis, indicated that microbial communities in the field soil do not necessarily differ largely between conventional and organic farming systems.
  • Markussen, Trine; Happel, Elisabeth M.; Teikari, Jonna Emilia; Huchaiah, Vimala; Alneberg, Johannes; Andersson, Anders F.; Sivonen, Anna Kaarina; Riemann, Lasee; Middelboe, Mathias; Kisand, Veljo (2018)
    Bacteria are major drivers of biogeochemical nutrient cycles and energy fluxes in marine environments, yet how bacterial communities respond to environ- mental change is not well known. Metagenomes allow examination of genetic responses of the entire micro- bial community to environmental change. However, it is challenging to link metagenomes directly to bio- geochemical process rates. Here, we investigate metagenomic responses in natural bacterioplankton communities to simulated environmental stressors in the Baltic Sea, including increased river water input, increased nutrient concentration, and reduced oxy- gen level. This allowed us to identify informative pro- karyotic gene markers, responding to environmental perturbation. Our results demonstrate that metage- nomic and metabolic changes in bacterial communi- ties in response to environmental stressors are influenced both by the initial community composition and by the biogeochemical factors shaping the func- tional response. Furthermore, the different sources of dissolved organic matter (DOM) had the largest impact on metagenomic blueprint. Most prominently, changes in DOM loads influenced specific trans- porter types reflecting the substrate availability and DOC assimilation and consumption pathways. The results provide new knowledge for developing models of ecosystem structure and biogeochemical cycling in future climate change scenarios and advance our exploration of the potential use of marine microorganisms as markers for environmen- tal conditions.
  • Yan, Lijuan; Yu, Dan; Hui, Nan; Naanuri, Eve; Viggor, Signe; Gafarov, Arslan; Sokolov, Sergei L; Heinaru, Ain; Romantschuk, Martin L. (2018)
    The Baltic Sea is vulnerable to environmental changes. With the increasing shipping activities, the risk of oil spills remains high. Archaea are widely distributed in many environments. However, the distribution and the response of archaeal communities to oil contamination have rarely been investigated in brackish habitats. Hence, we conducted a survey to investigate the distribution, diversity, composition, and species interactions of indigenous archaeal communities at oil-contaminated sites along the coast of the Gulf of Finland (GoF) using high-throughput sequencing. Surface water and littoral sediment samples were collected at presumably oil-contaminated (oil distribution facilities) and clean sites along the coastline of the GoF in the winter 2015 and the summer 2016. Another three samples of open sea surface water were taken as offshore references. Of Archaea, Euryarchaeota dominated in the surface water and the littoral sediment of the coast of the GoF, followed by Crenarchaeota (including Thaumarchaeota, Thermoprotei, and Korarchaeota based on the Greengenes database used). The unclassified sequences accounted for 5.62% of the total archaeal sequences. Our study revealed a strong dependence of the archaeal community composition on environmental variables (e.g., salinity, pH, oil concentration, TOM, electrical conductivity, and total DNA concentration) in both littoral sediment and coastal water in the GoF. The composition of archaeal communities was season and ecosystem dependent. Archaea was highly diverse in the three ecosystems (littoral sediment, coastal water, and open sea water). Littoral sediment harbored the highest diversity of archaea. Oil was often detected in the littoral sediment but rarely detected in water at those presumably contaminated sites. Although the composition of archaeal community in the littoral sediment was sensitive to low-input oil contamination, the unchanged putative functional profiles and increased interconnectivity of the archaeal core species network plausibly revealed resilience and the potential for oil degradation. Halobacteriaceae and putative cytochrome P450 pathways were significantly enriched in the oil-contaminated littoral sediment.The archaeal taxa formed highly interconnected and interactive networks, in which Halobacteriaceae, Thermococcus, and methanogens were the main components, implying a potential relevant trophic connection between hydrocarbon degradation, methanogenesis, sulfate reduction, and/or fermentative growth.
  • Hui, Nan; Liu, Xinxin; Kotze, D. Johan; Jumpponen, Ari; Francini, Gaia; Setala, Heikki (2017)
    Ectomycorrhizal (ECM) fungi are important mutualists for the growth and health of most boreal trees. Forest age and its host species composition can impact the composition of ECM fungal communities. Although plentiful empirical data exist for forested environments, the effects of established vegetation and its successional trajectories on ECM fungi in urban greenspaces remain poorly understood. We analyzed ECM fungi in 5 control forests and 41 urban parks of two plant functional groups (conifer and broadleaf trees) and in three age categories (10, similar to 50, and > 100 years old) in southern Finland. Our results show that although ECM fungal richness was marginally greater in forests than in urban parks, urban parks still hosted rich and diverse ECM fungal communities. ECM fungal community composition differed between the two habitats but was driven by taxon rank order reordering, as key ECM fungal taxa remained largely the same. In parks, the ECM communities differed between conifer and broadleaf trees. The successional trajectories of ECM fungi, as inferred in relation to the time since park construction, differed among the conifers and broadleaf trees: the ECM fungal communities changed over time under the conifers, whereas communities under broadleaf trees provided no evidence for such age-related effects. Our data show that plant-ECM fungus interactions in urban parks, in spite of being constructed environments, are surprisingly similar in richness to those in natural forests. This suggests that the presence of host trees, rather than soil characteristics or even disturbance regime of the system, determine ECM fungal community structure and diversity. IMPORTANCE In urban environments, soil and trees improve environmental quality and provide essential ecosystem services. ECM fungi enhance plant growth and performance, increasing plant nutrient acquisition and protecting plants against toxic compounds. Recent evidence indicates that soil-inhabiting fungal communities, including ECM and saprotrophic fungi, in urban parks are affected by plant functional type and park age. However, ECM fungal diversity and its responses to urban stress, plant functional type, or park age remain unknown. The significance of our study is in identifying, in greater detail, the responses of ECM fungi in the rhizospheres of conifer and broadleaf trees in urban parks. This will greatly enhance our knowledge of ECM fungal communities under urban stresses, and the findings can be utilized by urban planners to improve urban ecosystem services.
  • Jauhiainen, Jyrki; Kerojoki, Otto; Silvennoinen, Hanna; Limin, Suwido; Vasander, Harri (2014)
    Vast areas of deforested tropical peatlands do not receive noteworthy shading by vegetation, which increases the amount of solar radiation reaching the peat surface. Peat temperature dynamics and heterotrophic carbon dioxide (CO2), nitrous oxide (N2O) and methane (CH4) fluxes were monitored under four shading conditions, i.e. unshaded, 28%, 51% and 90% shading at experiment sites established on reclaimed fallow agricultural- and degraded sites in Central Kalimantan, Indonesia. Groundwater tables on the sites were at about 50 cm depth, the sites were maintained vegetation free and root ingrowth to gas flux monitoring locations was prevented. Half of the four shading areas received NPK-fertilization 50 kg ha−1 for each of N, P and K during the experiment and the other half was unfertilized. Increases in shading created a lasting decrease in peat temperatures, and decreased diurnal temperature fluctuations, in comparison to less shaded plots. The largest peat temperature difference in the topmost 50 cm peat profile was between the unshaded and 90% shaded surface, where the average temperatures at 5 cm depth differed up to 3.7 °C, and diurnal temperatures at 5 cm depth varied up to 4.2 °C in the unshaded and 0.4 °C in the 90% shaded conditions. Highest impacts on the heterotrophic CO2 fluxes caused by the treatments were on agricultural land, where 90% shading from the full exposure resulted in a 33% lower CO2 emission average on the unfertilized plots and a 66% lower emission average on the fertilized plots. Correlation between peat temperature and CO2 flux suggested an approximately 8% (unfertilized) and 25% (fertilized) emissions change for each 1 °C temperature change at 5 cm depth on the agricultural land. CO2 flux responses to the treatments remained low on degraded peatland. Fertilized conditions negatively correlated with N2O efflux with increases in temperature, suggesting a 12–36% lower efflux for each 1 °C increase in peat temperature (at 5 cm depth) at the sites. Despite the apparently similar landscapes of fallow agricultural land and degraded peatland sites, the differences in greenhouse gas dynamics are expected to be an outcome of the long-term management differences.
  • Zanella, Augusto; Berg, Björn; Ponge, Jean-Francois; Kemmers, Rolf H. (2017)
    Humusica 1 and 2 Applied Soil Ecology Special issues are field guides for humipedon classification. Contrary to other similar manuals dedicated to soil, the objects that one can describe with these guides are living, dynamic, functional, and relatively independent soil units. This is the reason to why the authors dedicated the whole article number 2 to functional considerations even before readers could go in the field and face the matter to be classified. Experienced lectors can overstep many of the sections reported in this article. If the titles of sections "1 A functional classification", "2 What is a humus system?" and "3 Energetic considerations in terrestrial systems" stimulate the reader's curiosity, then we suggest to pass through them. Otherwise, only section "4 Climatic, plant litter, or nutritional constraints?" is crucial. Readers will understand how the soil works in terms of litter and Carbon accumulation, which one(s) among climatic, vegetational, or geological factors that intervene and strongly affect the formation processes of terrestrial (oxygenated) soils. The article concludes with a debate about a tergiversated question: can temperature influence humus decomposition? Preceding statements were used for explaining how the biological soil net can store in the soil a maximum of energy in the form of SOM, by raising a plateau partially independent of climatic conditions.
  • van Leeuwe, Maria A.; Tedesco, Letizia; Arrigo, Kevin R.; Assmy, Philipp; Campbell, Karley; Meiners, Klaus M.; Rintala, Janne-Markus; Selz, Virginia; Thomas, David N.; Stefels, Jacqueline (2018)
    Sea ice is one the largest biomes on earth, yet it is poorly described by biogeochemical and climate models. In this paper, published and unpublished data on sympagic (ice-associated) algal biodiversity and productivity have been compiled from more than 300 sea-ice cores and organized into a systematic framework. Significant patterns in microalgal community structure emerged from this framework. Autotrophic flagellates characterize surface communities, interior communities consist of mixed microalgal populations and pennate diatoms dominate bottom communities. There is overlap between landfast and pack-ice communities, which supports the hypothesis that sympagic microalgae originate from the pelagic environment. Distribution in the Arctic is sometimes quite different compared to the Antarctic. This difference may be related to the time of sampling or lack of dedicated studies. Seasonality has a significant impact on species distribution, with a potentially greater role for flagellates and centric diatoms in early spring. The role of sea-ice algae in seeding pelagic blooms remains uncertain. Photosynthesis in sea ice is mainly controlled by environmental factors on a small scale and therefore cannot be linked to specific ice types. Overall, sea-ice communities show a high capacity for photoacclimation but low maximum productivity compared to pelagic phytoplankton. Low carbon assimilation rates probably result from adaptation to extreme conditions of reduced light and temperature in winter. We hypothesize that in the near future, bottom communities will develop earlier in the season and develop more biomass over a shorter period of time as light penetration increases due to the thinning of sea ice. The Arctic is already witnessing changes. The shift forward in time of the algal bloom can result in a mismatch in trophic relations, but the biogeochemical consequences are still hard to predict. With this paper we provide a number of parameters required to improve the reliability of sea-ice biogeochemical models.
  • Berner, Annina Zihler; Fuentes, Susana; Dostal, Alexandra; Payne, Amanda N.; Gutierrez, Pamela Vazquez; Chassard, Christophe; Grattepanche, Franck; de Vos, Willem M.; Lacroix, Christophe (2013)
  • Hui, Nan; Liu, Xinxin; Jumpponen, Ari; Setälä, Heikki; Kotze, D. Johan; Biktasheva, Liliya; Romantschuk, Martin (2018)
    Although soil-inhabiting fungi can affect tree health and biomass production in managed and pristine forests, little is known about the sensitivity of the plant-fungal associations to long-term changes in land use. We aimed to investigate how reforestation of farmlands change soil characteristics and affected the recovery of soil fungal functional guilds. We examined edaphic conditions and fungal communities (Illumina Sequencing) in three land-use types: primary forests (PF), secondary forests (SF, established over two decades ago) and active farmlands during May, July and September in Wuying, China. Edaphic conditions and general fungal communities varied with land-use. Interestingly, overall fungal diversity was higher in soils at the farmland than at the forested sites, possibly as a result of recurring disturbances (tilling) allowing competitive release as described by the intermediate disturbance hypothesis. Although ectomycorrhizal fungal diversity and richness were marginally higher in PF than in SF, the latter still hosted surprisingly diverse and abundant ectomycorrhizal fungal communities. Reforestation largely restored fungal communities that were still in transition, as their composition in SF was distinct from that in PF. Our results highlight the ability of fungi grown in previously strongly managed agricultural land to rapidly respond to reforestation and thus provide support for forest trees.
  • Li, Honghong; Penttinen, Petri; Mikkonen, Anu; Stoddard, Frederick L.; Lindstrom, Kristina (2020)
    Pastures are an important part of crop and food systems in cold climates. Understanding how fertilization and plant species affect soil bacterial community diversity and composition is the key for understanding the role of soil bacteria in sustainable agriculture. To study the response of soil bacteria to different fertilization and cropping managements, a 3-year (2013-2015) field study was established. In the split-plot design, fertilizer treatment (unfertilized control, organic fertilizer, and synthetic fertilizer) was the main plot factor, and plant treatment [clear fallow, red clover (Trifolium pratense), timothy (Phleum pratense), and a mixture of red clover and timothy] was the sub-plot factor. Soil bacterial community diversity and composition, soil properties, and crop growth were investigated through two growing seasons in 2014 and 2015, with different nitrogen input levels. The community diversity measures (richness, Shannon diversity, and Shannon evenness) and composition changed over time (P<0.05) and at different time scales. The community diversity was lower in 2014 than in 2015. The temporal differences were greater than the differences between treatments. The overall correlations of Shannon diversity to soil pH, NO3-, NH4+, and surplus nitrogen were positive and that of bacterial richness to crop dry matter yield was negative (P<0.05). The major differences in diversity and community composition were found between fallow and planted treatments and between organic and synthetic fertilizer treatments. The differences between the planted plots were restricted to individual operational taxonomic units (OTUs). Soil moisture, total carbon content, and total nitrogen content correlated consistently with the community composition (P<0.05). Compared to the unfertilized control, the nitrogen fertilizer loading enhanced the temporal change of community composition in pure timothy and in the mixture more than that in red clover, which further emphasizes the complexity of interactions between fertilization and cropping treatments on soil bacteria.
  • Lyra, Christina; Sinkko, Hanna-Mari; Rantanen, Matias; Paulin, Lars; Kotilainen, Aarno (2013)
  • Hiltunen, Lea H.; Tarvainen, Oili; Kelloniemi, Jani; Tanskanen, Jaakko; Karhu, Jouni; Valkonen, Jari P. T. (2021)
    Disease suppressive soils are important for managing soil-borne diseases that cannot be controlled with chemicals. One such disease is the potato common scab caused by Streptomyces species. Suppressiveness against common scab can develop spontaneously in fields where potato is grown for years without interruption, and this has been attributed to non-pathogenic Streptomyces strains. Streptomyces spp. have been used as inoculants in biological control, but their long-term effects have gained less attention. In our previous studies, a nonpathogenic Streptomyces strain (Str272) isolated from a potato common scab lesion suppressed common scab in field trials lasting over 5 years. In this study, bacterial communities in the tuberosphere i.e. in the soil adjacent to potato tubers, were analysed by next generation sequencing (NGS). The aim was to compare bacterial communities in untreated control plots to those in which seed tubers were treated with Str272 in one or several growing seasons. Str272 applications increased soil bacterial diversity and affected the bacterial composition in the potato tuberosphere. The most pronounced differences were observed between the untreated control and the treatments in which the antagonist had been applied in three or four consecutive years. The differences remained similar until the following growing season. Bacterial composition after repeated antagonist applications was associated with lower common scab severity. The antagonist applications had no or only slight effect on the number or abundance of OTUs belonging to Actinobacteria or Streptomyces, and no differences in quantities of pathogenic Streptomyces populations were detected by qPCR. This indicates that suppression of common scab by Str272 may not be based on direct effect on the common scab pathogens but is more likely to be associated with the alterations of the soil bacterial community. The most abundant bacteria phyla in the potato tuberosphere were Actinobacteria, Proteobacteria and Acidobacteria. However, the OTUs responding greatest to the antagonist treatments belonged to Bacterioidetes and Gemmatimonadetes. Results indicate that repeated applications of Str272 can change the bacterial community in the potato tuberosphere and lead to development of soil that is suppressive against potato common scab for several growing seasons after the last application.
  • Coda, Rossana; Kianjam, Maryam; Pontonio, Erica; Verni, Michela; Di Cagno, Raffaella; Katina, Kati; Rizzello, Carlo Giuseppe; Gobbetti, Marco (2017)
    The microbial ecology of faba bean sourdoughs obtained from an Italian (Ita) and a Finnish (Fi) cultivar, belonging respectively to Vicia faba major and V. faba minor groups, was described by 16S rRNA gene pyrosequencing and culture -dependent analysis. The sourdoughs were propagated with traditional backslapping procedure throughout 14 days. Higher microbial diversity was found in the sourdough deriving from V. faba minor (Fi), still containing residual hulls after the milling procedure. After 2 days of propagation, the microbial profile of Ita sourdough was characterized by the dominance of the genera Pediococcus, Leuconostoc and Weissella, while the genera Lactococcus, Lactobacillus and Escherichia, as well as Enterobacteriaceae were present in Fi sourdoughs. Yeasts were in very low cell density until the second backslopping and were not anymore found after this time by plate count or pyrosequencing analysis. Among the lactic acid bacteria isolates, Pediococcus pentosaceus, Leuconostoc mesenteroides and Weissella koreensis had the highest frequency of occurrence in both the sourdoughs. Lactobacillus sakei was the only lactobacillus isolated from the first to the last propagation day in Fi sourdough. According to microbiological and acidification properties, the maturity of the sourdoughs was reached after 5 days. The presence of hulls and the different microbial composition reflected on biochemical characteristics of Fi sourdoughs, including acidification and phenolic compounds. Moreover, proteolysis in Fi sourdough was more intense compared to Ita. The microbial dynamic of the faba bean sourdoughs showed some differences with the most studied cereal sourdoughs. (C) 2017 Elsevier B.V. All rights reserved.
  • Thrall, Peter H.; Laine, Anna-Liisa; Broadhurst, Linda M.; Bagnall, David J.; Brockwell, John (2011)
  • Hui, Nan; Parajuli, Anirudra; Puhakka, Riikka; Grönroos, Mira; Roslund, Marja; Vari, Heli; Selonen, Ville A. O.; Yan, Guoyang; Siter, Nathan; Nurminen, Noora; Oikarinen, Sami; Laitinen, Olli; Rajaniemi, Juho; Hyöty, Heikki; Sinkkonen, Aki (2019)
    An agricultural environment and exposure to diverse environmental microbiota has been suggested to confer protection against immune-mediated disorders. As an agricultural environment may have a protective role, it is crucial to determine whether the limiting factors in the transfer of environmental microbiota indoors are the same in the agricultural and urban environments. We explored how sampling month, garden diversity and animal ownership affected the indoor-transfer of environmental microbial community. We collected litter from standardized doormats used for 2 weeks in June and August 2015 and February 2016 and identified bacterial phylotypes using 16S rRNA Illumina MiSeq sequencing. In February, the diversity and richness of the whole bacterial community and the relative abundance of environment-associated taxa were reduced, whereas human-associated taxa and genera containing opportunistic pathogens were enriched in the doormats. In summer, the relative abundances of several taxa associated previously with beneficial health effects were higher, particularly in agricultural areas. Surprisingly, the importance of vegetation on doormat microbiota was more observable in February, which may have resulted from snow cover that prevented contact with microbes in soil. Animal ownership increased the prevalence of genera Bacteroides and Acinetobacter in rural doormats. These findings underline the roles of season, living environment and lifestyle in the temporal variations in the environmental microbial community carried indoors. As reduced contact with diverse microbiota is a potential reason for immune system dysfunction, the results may have important implications in the etiology of immune-mediated, non-communicable diseases.
  • Lindstrom, Stafva; Timonen, Sari; Sundstrom, Liselotte (2021)
    In a subarctic climate, the seasonal shifts in temperature, precipitation, and plant cover drive the temporal changes in the microbial communities in the topsoil, forcing soil microbes to adapt or decline. Many organisms, such as mound-building ants, survive the cold winter owing to the favorable microclimate in their nest mounds. We have previously shown that the microbial communities in the nest of the ant Formica exsecta are significantly different from those in the surrounding bulk soil. In the current study, we identified taxa, which were consistently present in the nests over a study period of three years. Some taxa were also significantly enriched in the nest samples compared with spatially corresponding reference soils. We show that the bacterial communities in ant nests are temporally stable across years, whereas the fungal communities show greater variation. It seems that the activities of the ants contribute to unique biochemical processes in the secluded nest environment, and create opportunities for symbiotic interactions between the ants and the microbes. Over time, the microbial communities may come to diverge, due to drift and selection, especially given the long lifespan (up to 30 years) of the ant colonies.
  • Wei, Lili; Vosatka, Miroslav; Cai, Bangping; Ding, Jing; Lu, Changyi; Xu, Jinghua; Yan, Wenfei; Li, Yuhong; Liu, Chaoxiang (2019)
    Arbuscular mycorrhizal fungi (AMF) are widespread in terrestrial ecosystems. In addition to their contributions to plant nutrient uptake, AMF also provide many ecological functions including regulation of soil C dynamics. However, both stimulating and retarding soil organic decomposition by AMF have been observed. Here we discuss the possible reasons for such a contradiction. Arbuscular mycorrhizal fungi contribute to soil aggregation mainly through hyphal enmeshment, saprotrophic suppression, and production of glomalin-related soil proteins, while AMF can also stimulate organic decomposition through promoting degradative enzymes, modifying root production and activity, and/or through regulating the microbial community in the mycorrhizosphere and hyphosphere. The role of AMF in C decomposition is strongly dependent on the quality and quantity of different soil C pools. Arbuscular mycorrhizal fungi can stimulate fresh residue decomposition initially through stimulating the decomposition of fresh residues (particularly those having high C/N ratio), whereas for older or decomposed soil organic C, AMF tend to suppress decomposition by promoting soil aggregation. Under elevated CO2 (eCO(2)), AMF show additive effects on residue decomposition, priming effects, and changes in soil a regation. Despite organic decomposition rates differing in the short term and long term following litter experiments, our discussion highlights the role of AMF in organic C dynamics. We hypothesize that AMF would benefit soil C gain in the long term and thereby predict that disturbances that impacts negatively on AMF, such as tillage, residue burning, fertilization, and fungicide application, would lead to soil C decline particularly under eCO(2).