Jaak Truu

• PhD
• Professor (Full) at University of Tartu

Microbiome research, the study of microbial communities in diverse environments, has seen significant advances due to the integration of deep learning (DL) methods. These computational techniques have become essential for addressing the inherent complexity and high-dimensionality of microbiome data, which consist of different types of omics dataset...

Microbial Fuel Cell (MFC) technology has become an alternative platform for bioremediation and power generation. Herein, three different potentials (−0.3 V, 0.0 V, +0.3 V vs Ag/AgCl) were used to improve the ability of the microbial community to degrade diesel fuel and assess their long-term community behaviour. The maximum current density was obse...

Bioelectrochemical systems offer unique opportunities to remove recalcitrant environmental pollutants in a net positive energy process, although it remains challenging because of the toxic character of such compounds. In this study, microbial fuel cell (MFC) technology was applied to investigate the benzene degradation process for more than 160 day...

The human microbiome has become an area of intense research due to its potential impact on human health. However, the analysis and interpretation of this data have proven to be challenging due to its complexity and high dimensionality. Machine learning (ML) algorithms can process vast amounts of data to uncover informative patterns and relationship...

During the World Wars large quantities of phenylarsenic chemical warfare agents (CWAs) were dumped in the Baltic Sea. Many transformation products of these chemicals have been identified, but the pathways that produce the found chemicals has not been investigated. Here we studied the biotic and abiotic transformation of phenylarsenic CWAs under oxi...

The rapid development of machine learning (ML) techniques has opened up the data-dense field of microbiome research for novel therapeutic, diagnostic, and prognostic applications targeting a wide range of disorders, which could substantially improve healthcare practices in the era of precision medicine. However, several challenges must be addressed...

Background and aims: Response of subarctic grassland's belowground to soil warming is key for understanding ecosystem's adaptation to future climate. Functionally different belowground plant organs can respond differently to changes in soil temperature (Ts). We aimed to understand the belowground adaptation mechanisms by analyzing the dynamics and...

Petroleum hydrocarbons pose a substantial threat to marine ecosystems [...]

Estonian sedimentary deposits (e.g., graptolite argillite) with relatively high content oforganic matter and metals (V, Mo, U and Zn) are habitat for microorganisms. Metalsexist in argillite as sulfides, in the composition of organometallic compounds or insilicate minerals. While the role of pyrite oxidizing microorganisms in bioleaching ofmetals i...

Estonian sedimentary deposits (e.g., graptolite argillite) with relatively high content of organic matter and metals (V, Mo, U and Zn) are habitat for microorganisms. Metals exist in argillite as sulfides, in the composition of organometallic compounds or in silicate minerals. While the role of pyrite oxidizing microorganisms in bioleaching of meta...

Soil invertebrates are key to decomposition, a central ecosystem process related to soil health. In many temperate areas climate change will decrease soil water content, which strongly modulates biological activity. However, data are lacking on how shifts in rainfall patterns affect soil biota and the ecosystem processes they provide. Here, we used...

Engineered nanoparticles, including silver nanoparticles (AgNPs), are released into the environment mainly through wastewater treatment systems. Knowledge of the impact of AgNPs on the abundance and removal efficiency of antibiotic resistance genes (ARGs) in wastewater treatment facilities, including constructed wetlands (CWs), is essential in the...

Dispersants have been used in several oil spill accidents, but little information is available on their effectiveness in Baltic Sea conditions with low salinity and cold seawater. This study investigated the effects of dispersant use on petroleum hydrocarbon biodegradation rates and bacterial community structures. Microcosm experiments were conduct...

Methane (CH4) emissions generated from waste management facilities represent a serious global warming concern. The objective of this study was to monitor a fully instrumented biocover capable of abating fugitive CH4 emissions from a closed landfill located at Kudjape, Saaremaa Island, Estonia. This investigation documented the alteration in the emi...

Agricultural application of plant-beneficial bacteria to improve crop yield and alleviate the stress caused by environmental conditions, pests, and pathogens is gaining popularity. However, before using these bacterial strains in plant experiments, their environmental stress responses and plant health improvement potential should be examined. In th...

Silver nanoparticles (AgNPs) threaten human and ecosystem health, and are among the most widely used engineered nanomaterials that reach wastewater during production, usage, and disposal phases. This study evaluated the effect of a 100-fold increase in collargol (protein-coated AgNP) and Ag⁺ ions concentrations in municipal wastewater on the microb...

In this study, the effect of seed treatment with Achromobacter xylosoxidans AUM54 and glycolipid-type biosurfactants produced by this bacterial strain to suppress Ralstonia solanacearum, which causes bacterial wilt in tomato plants, was investigated. Applying biosurfactant in combination with the biosurfactant-producing bacteria reduced the R. sola...

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...

Soil biodiversity constitutes the biological pillars of ecosystem services provided by soils worldwide. Soil life is threatened by intense agricultural management and shifts in climatic conditions as two important global change drivers which are not often jointly studied under field conditions. We addressed the effects of experimental short-term dr...

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 degra...

The abundance and taxonomic composition of ammonia‐oxidizing archaea (AOA) was assessed in paddy soils receiving more than 50 years of fertilization with and without inorganic N. The inorganic N fertilized treatments were: NPK and NPK + CO [Nitrogen (N), phosphorus (P), potassium (K) and compost (CO)]. The treatments without inorganic N were: CO, P...

The effluents of wastewater treatment plants (WWTPs) are major contributors of nutrients, microbes—including those carrying antibiotic resistance genes (ARGs)—and pathogens to receiving waterbodies. The effect of the effluent of a small-scale activated sludge WWTP treating municipal wastewater on the composition and abundance of the microbial commu...

The human microbiome has emerged as a central research topic in human biology and biomedicine. Current microbiome studies generate high-throughput omics data across different body sites, populations, and life stages. Many of the challenges in microbiome research are similar to other high-throughput studies, the quantitative analyses need to address...

The number of microbiome-related studies has notably increased the availability of data on human microbiome composition and function. These studies provide the essential material to deeply explore host-microbiome associations and their relation to the development and progression of various complex diseases. Improved data-analytical tools are needed...

: This study assessed the potential of Bacillus endophyticus PB3, Bacillus altitudinis PB46, and Bacillus megaterium PB50 to induce drought tolerance in a susceptible rice cultivar. The leaves of the potted rice plants subjected to physical drought stress for 10 days during the flowering stage were inoculated with single-strain suspensions. Control...

Peatlands are unique wetland ecosystems that cover approximately 3% of the world’s land area and are mostly located in boreal and temperate regions. Around 15 Mha of these peatlands have been drained for forestry during the last century. This study investigated soil archaeal and bacterial community structure and abundance, as well as the abundance...

Drought and agricultural management influence soil microorganisms with unknown consequences for the functioning of agroecosystems. We simulated drought periods in organic (biodynamic) and conventional wheat fields and monitored effects on soil water content, microorganisms and crops. Above the wilting point, water content and microbial respiration...

Solid organic waste is a significant source of antibiotic resistance genes (ARGs) and effective treatment strategies are urgently required to limit the spread of antimicrobial resistance. Here we studied ARG diversity and abundance as well as the relationship between antibiotic resistome and microbial community structure within a lab-scale solid-st...

The integrated remediation plan of the Laguja landfill, Estonia, includes creation of aconstructed wetland for treatment of landfill leachate. A mesocosm experiment wasconducted in order to estimate the impact of different plant species on purification efficiencyof wetland. The quality of water in mesocosms was monitored during vegetation period. A...

Field and laboratory experiments were carried out in order to estimate the suitability ofphytoremediation and bioaugmentation for oil shale chemical industry solid waste (semicoke) dump area remediation as well as influence of plants and laboratory selecteddegradative bacterial strains on the microbial communities in semi-coke, Field test plots (ea...

The major environmental problem in the northeastern Estonia is the semi-coke mounds in oilshale industry areas, Alternatives to the chemical methods (sorption, ozonation) for removingxenobiotic compounds from leachate are biological methods, like bioaugmentation, where theproperly selected microorganisms are used. Determination of the kinetic const...

In the present study, a combined treatment strategy involving the addition of rhamnolipid, rhamnolipid-producing bacteria (Shewanella sp. BS4) and a native soil microbial community for the remediation of hydrocarbon-contaminated soil under pilot-scale conditions was adopted. The isolate BS4 (rhl+), demonstrating the highest emulsification activity...

This article introduces the EU Horizon 2020 research project GRACE (Integrated oil spill response actions and environmental effects), which focuses on a holistic approach towards investigating and understanding the hazardous impact of oil spills and the environmental impacts and benefits of a suite of marine oil spill response technologies in the c...

The phenol-rich leachate from semi-coke mounds formed as a by-product of oil-shaleprocessing is discharged via channels and rivers Kohtla and Purtse into the Baltic Sea withoutany treatment. The leachate from processed oil shale contains several organic and inorganiccompounds (oil fractions, sulphides, polycyclic aromatic hydrocarbons). The impact...

Although the production of oil shale energy and oil has decreased steadily during the last years with a corresponding decrease in wastes, the semi-coke mounds constitute one of the major adverse environmental challenges in Estonia The processed oil shale (semicoke) contains several organic and inorganic compounds (oil fractions, sulphides, phenolic...

Background Oral microbiome has significant impact on both oral and general health. Polyols have been promoted as sugar substitutes in prevention of oral diseases. We aimed to reveal the effect of candies containing erythritol, xylitol or control (sorbitol) on salivary microbiome. Methods Ninety children (11.3 ± 0.6 years) consumed candies during 3...

Cover crops play an increasingly important role in improving soil quality, reducing agricultural inputs and improving environmental sustainability. The main objectives of this critical global review and systematic analysis were to assess cover crop practices in the context of their impacts on nitrogen leaching, net greenhouse gas balances (NGHGB) a...

Antimicrobial resistance is a globally recognized public health risk. High incidence of antibiotic resistant bacteria and antibiotic resistance genes (ARGs) in solid organic waste necessitates the development of effective treatment strategies. The objective of this study was to assess ARG diversity and abundance as well as the relationship between...

The objectives of this study were to determine the biofilm microbial activity and bacterial community structure and successions in greywater treatment filters and to relate the treatment efficiency to the bacterial community parameters. This 10-month study was performed in a newly established experimental system for domestic greywater treatment tha...

Silicon (Si) is widely used in improving crop yield, but effect of its application on soil bacterial community composition is poorly known. Quantitative PCR and high-throughput sequencing targeting the bacterial 16S rRNA gene were employed to characterize the bacterial community composition of long-term fertilized paddy soils treated with nitrogen...

The effects of phosphorus (P) availability on soil microbial community and its functional responses have not been widely explored till date. The present study involved high throughput sequencing of 16S rRNA to investigate the bacterial community structure, size and function in long-term fertilized paddy soils that received P fertilizers (+ P) and c...

Wastewater treatment systems receiving municipal wastewater are major dissemination nodes of antibiotic resistance genes (ARGs) between anthropogenic and natural environments. This study examined the fate of antibiotic resistome and class 1-3 integron-integrase genes in photobioreactors that were treating municipal wastewater diluted (70/30) with l...

Biochar has shown great potential as an amendment to improve soil quality and promote plant growth, as well as to adsorb pollutants from water. However, information about the effect of biochar on the wastewater treatment efficiency in horizontal subsurface flow (HSSF) constructed wetlands (CWs) is still scarce. In this study, we assessed the effect...

The original version of this Article contained an error in the first sentence of the Acknowledgements section, which incorrectly referred to the Estonian Research Council grant identifier as "PUTJD618". The correct version replaces the grant identifier with "PUTJD619". This has been corrected in both the PDF and HTML versions of the Article.

The pollution of agricultural soils by the heavy metals affects the productivity of the land and has an impact on the quality of the surrounding ecosystems. This study investigated the bacterial community structure in the heavy metal contaminated sites along a smelter and a distantly located paddy field to elucidate the factors that are related to...

Nitrous oxide (N2O) is a powerful greenhouse gas and the main driver of stratospheric ozone depletion. Since soils are the largest source of N2O, predicting soil response to changes in climate or land use is central to understanding and managing N2O. Here we find that N2O flux can be predicted by models incorporating soil nitrate concentration (NO3...

Tropical peatlands, which play a crucial role in the maintenance of different ecosystem services, are increasingly drained for agriculture, forestry, peat extraction and human settlement purposes. The present study investigated the differences between natural and drained sites of a tropical peatland in the community structure of soil bacteria and a...

- 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 betwee...

Soil microbes play a fundamental role in forest ecosystems and respond rapidly to changes in the environment. Simultaneously with the temperature increase the climate change scenarios also predict an intensified hydrological cycle for the Baltic Sea runoff region. The aim of this study was to assess the effect of elevated air humidity on the top so...

Objectives: To profile the seminal microbiome applying next generation sequencing. Methods: Semen samples of 67 men were involved in the study (21 men with and 46 men without prostatitis). Seminal microbiomes were profiled applying the method that uses combinatorial sequence tags attached to polymerase chain reaction primers that amplify the rib...

The aim of this study was to analyse and identify preferred atmospheric circulation conditions for migratory birds during their spring arrival in Estonia (for Tartu and Kuressaare). A total of 47 circulation classifications and 42 common bird species were studied. The analysis identified a clear division of species into two general clusters accordi...

Dynamics of bacterial community abundance and structure of a newly established horizontal subsurface flow (HSSF) pilot-scale wetland were studied using high-throughput sequencing and quantitative polymerase chain reaction (PCR) methods. Bacterial community abundance increased rapidly within one month and stabilised thereafter in three replicate HSS...

This study examined physiochemical conditions and prokaryotic community structure (the bacterial and archaeal 16S rRNA genes and mcrA gene abundances and proportions), and evaluated the effect of reed canary grass cultivation and mineral fertilisation on these factors, in the 60 cm thick residual peat layer of experimental plots located on an aband...

The characteristics of the qPCR primer sets and programmes. (DOCX)

Statistically significant relationships between different gene parameters, and between gene parameters and means of the study years vegetation periods`soil physical parameters as well as methane emissions in three layers of the studied soil groups. (DOCX)

Statistical analyses. (DOCX)

Mean values and standard deviations of soil chemical parameters in different peat layers of the studied soil groups at the sampling times. (DOCX)

Statistically significant relationships between different gene parameters and soil chemical variables, and between gene parameters of different treatments in three layers. (DOCX)

Quantitative PCR. (DOCX)

Northern peatlands constitute a significant source of atmospheric methane (CH4). However, management of undisturbed peatlands, as well as the restoration of disturbed peatlands, will alter the exchange of CH4 with the atmosphere. The aim of this systematic review and meta-analysis was to collate and analyze published studies to improve our understa...

Previous pilot-scale studies have shown outstanding levels of efficiency in phosphorus removal by using hydrated oil shale ash (HOSA) sediments in horizontal subsurface flow (HSSF) filters with low greenhouse gas emissions. However, no long-term full-scale experiment has been conducted using this material. From September 2013 to December 2015, two...

The effect of inhibiting nitrification on algal growth and nutrient uptake was studied in photobioreactors treating municipal wastewater. As previous studies have indicated that algae prefer certain nitrogen species to others, and because nitrifying bacteria are inhibited by microalgae, it is important to shed more light on these interactions. In t...

This two-week anaerobic batch study evaluated 2,4,6-trinitrotoluene (TNT) removal efficiency from industrial pink water by (1) adsorption on low-cost adsorbent pine bark, and (2) adsorption coupled with TNT biotransformation by specialised microbial communities. Samples of the supernatant and acetonitrile extracts of pine bark were analysed by HPLC...

Artificial pulsing of water table is often used in horizontal subsurface flow (HSSF) constructed wetlands (CW) to enhance removal of BOD, COD, NH4 and total N utilization by bacteria. In 2008-2010 and during the experimental session in October-November 2012 we studied the impact of a fluctuating water table on the water purification efficiency and...

Phytoremediation is a technology that is based on the combined action of plants and their associated microbial communities to degrade, remove, transform, or immobilize toxic compounds located in soils, sediments, and more recentlyin polluted ground water andwastewater in treatment wetlands. Phytoremediation could be used to treat different types of...

Photobioreactors are a novel environmental technology that can produce biofuels with the simultaneous removal of nutrients and pollutants from wastewaters. The aim of this study was to evaluate the effect of lake water inoculation on the production of algal biomass and phylogenetic and functional structure of the algal and bacterial communities in...

Vaginal lactobacilli offer protection against microbiota imbalance and genitourinary tract infections. We compared vaginal lactobacilli in 50 Estonian women of child-bearing age applying culture-based methods, quantitative PCR and next-generation sequencing (NGS). The culture-based methods found three different lactobacilli: Lactobacillus crispatus...

The genital tract microbiome is tightly associated with reproductive health. Although many research studies have been performed on the vaginal microbiome, current knowledge of the male microbiome is scarce, and parallel studies examining couples are extremely rare. In this work, we aimed to compare seminal and vaginal microbiomes in couples and to...

Microalgae grown in photo-bioreactors can be a valuable source of biomass, especially when combined with wastewater treatment. While most published research has studied pure cultures, the consortia of algae and bacteria from wastewater have more complex community dynamics which affect both the biomass production and pollutant removal. In this paper...

Sorption and degradation are the primary processes controlling the efficacy and runoff contamination risk of agrochemicals. This study assessed the influence of two biochars, made from woodchips and straw at a pyrolysis temperature of 725 "C and applied to a loamy sand and a sandy soil in the concentration of 5.3 g 100g-1 sandy soil and 4.1 g 100g-...

Wader populations have been declining worldwide, providing a fundamental question as to which environmental factors limit population growth. Many studies have focused on the effects of habitat change on wader populations as a result of climate change, agricultural intensification or abandonment of arable land. However, there are few studies investi...

Known as biogeochemical hotspots in landscapes, riparian buffer zones exhibit considerable potential concerning mitigation of groundwater contaminants such as nitrate, but may in return enhance the risk for indirect N2O emission. Here we aim to assess and to compare two riparian grey alder forests in terms of gaseous N2O and N2 fluxes and dissolved...

Introduction: Chronic apical periodontitis (CAP) is a frequent condition that has a considerable effect on a patient's quality of life. We aimed to reveal root canal microbial communities in antibiotic-naive patients by applying Illumina sequencing (Illumina Inc, San Diego, CA). Methods: Samples were collected under strict aseptic conditions fro...

The human oral microbiota consists of more than thousand microbial species. Polyols, which are used in caries prevention as non-cariogenic sweeteners, could have an effect on the oral microbiome. Objective: The aim of the study was to assess the impact of daily consumption of three different polyols during 3-years on salivary microbiome. Method...