Differences in microbial community structure and nitrogen cycling in natural and drained tropical peatland soils

Funding Information: This was supported by the Estonian Research Council (grant IUT2-16); and the EU through the European Regional Development Fund through Centre of Excellence EcolChange and the European Social Fund (Doctoral School of Earth Sciences and Ecology). We would like to thank the PhD students participating in the field works.Peer reviewedPublisher PD

Soil Bacterial and Archaeal Communities and Their Potential to Perform N-Cycling Processes in Soils of Boreal Forests Growing on Well-Drained Peat

Funding Information: This study was supported by the Estonian Forest Management Centre, the Estonian Research Council grants PRG548, PRG916, and PRG352, WaterJPI-JC-2018_13 project, and Centres of Excellence Environ and EcolChange.Peer reviewedPublisher PD

Microbial community changes in TNT spiked soil bioremediation trial using biostimulation, phytoremediation and bioaugmentation

Trinitrotoluene (TNT), a commonly used explosive for military and industrial applications, can cause serious environmental pollution. 28-day laboratory pot experiment was carried out applying bioaugmentation using laboratory selected bacterial strains as inoculum, biostimulation with molasses and cabbage leaf extract, and phytoremediation using rye and blue fenugreek to study the effect of these treatments on TNT removal and changes in soil microbial community responsible for contaminant degradation. Chemical analyses revealed significant decreases in TNT concentrations, including reduction of some of the TNT to its amino derivates during the 28-day tests. The combination of bioaugmentation-biostimulation approach coupled with rye cultivation had the most profound effect on TNT degradation. Although plants enhanced the total microbial community abundance, blue fenugreek cultivation did not significantly affect the TNT degradation rate. The results from molecular analyses suggested the survival and elevation of the introduced bacterial strains throughout the experiment. First published online: 15 Feb 201

The bacterial community structure and functional profile in the heavy metal contaminated paddy soils, surrounding a nonferrous smelter in South Korea

Funding Information: The authors wish to thank the Basic Science Research Program of the National Research Foundation (NRF) under the Ministry of Education, Science and Technology (2015R1A2A1A05001885), South Korea for providing funding support toward the completion of this study. This study was supported partially by the Estonian Ministry of Education and Research (Grant IUT2–16), and by the European Regional Development Fund through the Centre of Excellence EcolChange. We thank Saale Truu for the assistance in computer graphics. Funding Information: National Research Foundation of Korea, Grant/Award Number: 2015R1A2A1A05001885; Estonian Ministry of Education and Research, Grant/ Award Number: IUT2–16; European Region Development Fund Publisher Copyright: © 2018 The Authors. Ecology and Evolution published by John Wiley & Sons Ltd. Copyright: Copyright 2018 Elsevier B.V., All rights reserved.Peer reviewedPublisher PD

Adaptive root foraging strategies along a boreal–temperate forest gradient

The tree root–mycorhizosphere plays a key role in resource uptake, but also in the adaptation of forests to changing environments. The adaptive foraging mechanisms of ectomycorrhizal (EcM) and fine roots of Picea abies, Pinus sylvestris and Betula pendula were evaluated along a gradient from temperate to subarctic boreal forest (38 sites between latitudes 48°N and 69°N) in Europe. Variables describing tree resource uptake structures and processes (absorptive fine root biomass and morphology, nitrogen (N) concentration in absorptive roots, extramatrical mycelium (EMM) biomass, community structure of root-associated EcM fungi, soil and rhizosphere bacteria) were used to analyse relationships between root system functional traits and climate, soil and stand characteristics. Absorptive fine root biomass per stand basal area increased significantly from temperate to boreal forests, coinciding with longer and thinner root tips with higher tissue density, smaller EMM biomass per root length and a shift in soil microbial community structure. The soil carbon (C) : N ratio was found to explain most of the variability in absorptive fine root and EMM biomass, root tissue density, N concentration and rhizosphere bacterial community structure. We suggest a concept of absorptive fine root foraging strategies involving both qualitative and quantitative changes in the root–mycorrhiza–bacteria continuum along climate and soil C : N gradients.Peer reviewe

Maakasutuse mõju mikroobikooslustele Eesti muldades

The ability of microorganisms to fulfill various important functions in soil enables the successful application of these organisms in different fields of environmental technology. Since microorganisms play a crucial role in degradation processes they are also able to detoxify different pollutants (toxicants), contributing in this way to the soil quality maintenance. On the other hand, microbial activities are strongly dependent on the nutritional and other chemical and physical conditions of the soil and respond rapidly to the changes in soil properties caused by land management or climate. The impact of different land use practices on the microbial communities in Estonian pedogenic - arable soils and anthropomorphic materials - sand filters of horizontal subsurface flow constructed wetland, and materials from opencast oil-shale mining areas with different applications was studied using microbiological and biochemical parameters. The response of the microbial community to soil management was dependent on soil type and other site specific conditions like the amount and form of nutrients in the soil. In pedogenic soils microbial communities had a bigger capacity to sustain its functions in changing conditions compared to the young communities in anthropomorphic materials. Arable soils (disturbed pedogenic soils) had a smaller and less active microbial biomass compared to natural soils. The sand filters of horizontal subsurface flow constructed wetland and abandoned mining soils from the anthropomorphic material group were characterized by the smallest microbial biomass among the studied soil groups while anthropomorphic materials from reclaimed mining areas presented intermediate (transitional) microbial biomass and activity values. Arable soils with different applications had well stabilized, effectively functioning microbial communities that could be separated from each other by their biomass and different activity parameters. Agricultural management practices include a range of different activities that specifically affect microbial biomass and its activity in arable soils. Soil microbes adapt to the conditions (artificial introduction of nutrients, destruction of soil structure by cultivation etc.) created by particular agricultural management type. Changes in land use force soil microbes to restructure their communities according to the new conditions and these changes can be monitored by shifts in microbiological parameters. Short-term pretreated municipal wastewater application to the abandoned agricultural soils had a weak positive effect on microbial communities. The microbial biomass was small, inefficient and its functional diversity was low in the domestic wastewater purifying sand filters of horizontal subsurface flow constructed wetland. The biggest microbial metabolic quotient among the studied soil groups suggested the dependence of these constructed systems on allochthonous nutrients and environmental factors. Muld on keeruline ja kompleksne keskkond, milles mikroorganismid on olulised ainete ringluses osalejad, muutes orgaanilistesse ühenditesse seotud mineraalained teistele organismidele kättesaadavaks. Mulla mikroobid osalevad nii orgaanilise aine moodustamises (huumusaine, glomaliin) kui ka suuremate mullas sisalduvate orgaanilise aine molekulide lagundamises väiksemateks subühikuteks ning on võimelised lagundama ka erinevaid mürkaineid. Teisalt on mikroorganismid tundlikud mitmesugustele keskkonnas toimuvatele muutustele, mille tõttu peetakse neid organisme headeks indikaatoriteks ka muldade seires. Käesoleva töös uuriti erineva maakasutuse mõju haritavatele pedogeensete muldade ja antropomorfsete materjalide (nagu mahajäetud põlevkivikarjääride pinnas ning kunstliku horisontaalvoolulise märgala liivafiltrid) mikroobikooslusetele ning võrrelda vastavate muldade mikrobioloogilisi parameetreid loodulike pedogeensete muldade vastavate parameetritega. Mahajäetud põlevkivikarjääride pinnaste puhul analüüsiti eraldi erinevate puuliikidega taimestatud ja taimestamata pinnaseid. Haritavate muldade hulgas vaadeldi aktiivseks põllumajanduslikuks tootmiseks kasutatavaid muldi, põllumajanduslikust kasutusest välja jäänud muldi, erinevate puuliikidega taimestatud endiseid põllumuldi ja olmereovee järelpuhastuseks kasutatavaid nii taimestatud kui taimestamata endiseid põllumuldi. Maakasutuse mõju hindamiseks mulla mikroobikooslustele kasutati erinevaid mikrobioloogilisi ja biokeemilisi parameetreid. Maakasutuse mõju hindamiseks koostati erinevate uuringute keemiliste, biokeemiliste ning mikrobioloogiliste analüüside tulemustest andmebaas. Tulemuste analüüs näitas, et maakasutus mõjutas oluliselt mulla mikrobioloogilisi ja biokeemilisi omadusi. Mikroobikoosluse vastus maakasutuse muutusele sõltus oluliselt mullatüübist ja kasvukohale omastest tingimustest. Haritavate muldade mikroobide biomass oli tunduvalt väiksem ja aktiivsus madalam kui looduslikes muldades. Kõige väiksem mikroobide biomass oli kunstliku märgala liivafiltrites ja mahajäetud karjääride pinnastes. Rekultiveeritud põlevkivikarjääride pinnaste mikroobikoosluste vastavad väärtused jäid looduslike ja haritavate muldade vahele. Haritavatele muldadele olid iseloomulikud hästi kohastunud ja stabiilselt funktsioneerivad mikroobikooslused. Põllumajanduslik praktika koosneb reast üksikutest tegevustest (orgaaniliste ja/või anorgaaniliste väetistega väetamine, kündmine, viljavaheldus, pestitsiididega töötlemine jne.), mille mõju mulla mikroobikoosluse biomassile ja aktiivsusele oli spetsiifiline. Põllumajanduslikust kasutusest välja jäänud muldadele ja mahajäetud karjääride pinnastele oli iseloomulik väike mikroobne biomass ja madal aktiivsus. Nende pinnaste taimestamine erinevate puuliikidega põhjustas biomassi tunduva suurenemise ning mikroobsete protsesside aktiviseerumise tänu taimejuurte toetusele. Eelpuhastatud olmeheitveega kastmine mõjutas positiivselt haritavate muldade mikroobseid protsesse – suurendas mikroobikoosluse funktsionaalset ja liigilist mitmekesisust endistes põllumuldades. Olmeheitvee mõjul suurenes mulla kaaliumi kontsentratsioon ja tõusis mikroobikoosluse fosfataasne aktiivsus. Kunstliku märgala horisontaalsete liivafiltrite mikroobide biomassid olid oluliselt väiksemad pedogeensete muldade vastavate näitajatega võrreldes

Microbial Community Dynamics during Biodegradation of Crude Oil and Its Response to Biostimulation in Svalbard Seawater at Low Temperature

The development of oil exploration activities and an increase in shipping in Arctic areas have increased the risk of oil spills in this cold marine environment. The objective of this experimental study was to assess the effect of biostimulation on microbial community abundance, structure,dynamics, and metabolic potential for oil hydrocarbon degradation in oil-contaminated Arctic seawater.The combination of amplicon-based and shotgun sequencing, together with the integration of genome-resolved metagenomics and omics data, was applied to assess microbial community structure and metabolic properties in naphthenic crude oil-amended microcosms. The comparison of estimates for oil-degrading microbial taxa obtained with different sequencing and taxonomic assignment methods showed substantial discrepancies between applied methods. Consequently,the data acquired with different methods was integrated for the analysis of microbial community structure, and amended with quantitative PCR, producing a more objective description of microbial community dynamics and evaluation of the effect of biostimulation on particular microbial taxa. Implementing biostimulation of the seawater microbial community with the addition of nutrients resulted in substantially elevated prokaryotic community abundance (103-fold), a distinctly different bacterial community structure from that in the initial seawater, 1.3-fold elevation in the normalized abundance of hydrocarbon degradation genes, and 12% enhancement of crude oil biodegradation.The bacterial communities in biostimulated microcosms after four months of incubation were dominated by Gammaproteobacterial genera Pseudomonas, Marinomonas, and Oleispira, which were succeeded by Cycloclasticus and Paraperlucidibaca after eight months of incubation. The majority of 195 compiled good-quality metagenome-assembled genomes (MAGs) exhibited diverse hydrocarbon degradation gene profiles. The results reveal that biostimulation with nutrients promotes naphthenic oil degradation in Arctic seawater, but this strategy alone might not be sufficient to effectively achieve bioremediation goals within a reasonable timeframe.publishedVersio

Assessment of Hydrocarbon Degradation Potential in Microbial Communities in Arctic Sea Ice

The anthropogenic release of oil hydrocarbons into the cold marine environment is an increasing concern due to the elevated usage of sea routes and the exploration of new oil drilling sites in Arctic areas. The aim of this study was to evaluate prokaryotic community structures and the genetic potential of hydrocarbon degradation in the metagenomes of seawater, sea ice, and crude oil encapsulating the sea ice of the Norwegian fjord, Ofotfjorden. Although the results indicated substantial differences between the structure of prokaryotic communities in seawater and sea ice, the crude oil encapsulating sea ice (SIO) showed increased abundances of many genera-containing hydrocarbon-degrading organisms, including Bermanella, Colwellia, and Glaciecola. Although the metagenome of seawater was rich in a variety of hydrocarbon degradation-related functional genes (HDGs) associated with the metabolism of n-alkanes, and mono- and polyaromatic hydrocarbons, most of the normalized gene counts were highest in the clean sea ice metagenome, whereas in SIO, these counts were the lowest. The long-chain alkane degradation gene almA was detected from all the studied metagenomes and its counts exceeded ladA and alkB counts in both sea ice metagenomes. In addition, almA was related to the most diverse group of prokaryotic genera. Almost all 18 goodand high-quality metagenome-assembled genomes (MAGs) had diverse HDGs profiles. The MAGs recovered from the SIO metagenome belonged to the abundant taxa, such as Glaciecola, Bermanella, and Rhodobacteracea, in this environment. The genera associated with HDGs were often previously known as hydrocarbon-degrading genera. However, a substantial number of new associations, either between already known hydrocarbon-degrading genera and new HDGs or between genera not known to contain hydrocarbon degraders and multiple HDGs, were found. The superimposition of the results of comparing HDG associations with taxonomy, the HDG profiles of MAGs, and the full genomes of organisms in the KEGG database suggest that the found relationships need further investigation and verification

Assessment of Hydrocarbon Degradation Potential in Microbial Communities in Arctic Sea Ice

The anthropogenic release of oil hydrocarbons into the cold marine environment is an increasing concern due to the elevated usage of sea routes and the exploration of new oil drilling sites in Arctic areas. The aim of this study was to evaluate prokaryotic community structures and the genetic potential of hydrocarbon degradation in the metagenomes of seawater, sea ice, and crude oil encapsulating the sea ice of the Norwegian fjord, Ofotfjorden. Although the results indicated substantial differences between the structure of prokaryotic communities in seawater and sea ice, the crude oil encapsulating sea ice (SIO) showed increased abundances of many genera-containing hydrocarbon-degrading organisms, including Bermanella, Colwellia, and Glaciecola. Although the metagenome of seawater was rich in a variety of hydrocarbon degradation-related functional genes (HDGs) associated with the metabolism of n-alkanes, and mono- and polyaromatic hydrocarbons, most of the normalized gene counts were highest in the clean sea ice metagenome, whereas in SIO, these counts were the lowest. The long-chain alkane degradation gene almA was detected from all the studied metagenomes and its counts exceeded ladA and alkB counts in both sea ice metagenomes. In addition, almA was related to the most diverse group of prokaryotic genera. Almost all 18 goodand high-quality metagenome-assembled genomes (MAGs) had diverse HDGs profiles. The MAGs recovered from the SIO metagenome belonged to the abundant taxa, such as Glaciecola, Bermanella, and Rhodobacteracea, in this environment. The genera associated with HDGs were often previously known as hydrocarbon-degrading genera. However, a substantial number of new associations, either between already known hydrocarbon-degrading genera and new HDGs or between genera not known to contain hydrocarbon degraders and multiple HDGs, were found. The superimposition of the results of comparing HDG associations with taxonomy, the HDG profiles of MAGs, and the full genomes of organisms in the KEGG database suggest that the found relationships need further investigation and verification.Assessment of Hydrocarbon Degradation Potential in Microbial Communities in Arctic Sea IcepublishedVersio