Functional Redundancy Secures Resilience of Chain Elongation Communities upon pH Shifts in Closed Bioreactor Ecosystems.

For anaerobic mixed cultures performing microbial chain elongation, it is unclear how pH alterations affect the abundance of key players, microbial interactions, and community functioning in terms of medium-chain carboxylate yields. We explored pH effects on mixed cultures enriched in continuous anaerobic bioreactors representing closed model ecosystems. Gradual pH increase from 5.5 to 6.5 induced dramatic shifts in community composition, whereas product range and yields returned to previous states after transient fluctuations. To understand community responses to pH perturbations over long-term reactor operation, we applied Aitchison PCA clustering, linear mixed-effects models, and random forest classification on 16S rRNA gene amplicon sequencing and process data. Different pH preferences of two key chain elongation species─one Clostridium IV species related to Ruminococcaceae bacterium CPB6 and one Clostridium sensu stricto species related to Clostridium luticellarii─were determined. Network analysis revealed positive correlations of Clostridium IV with lactic acid bacteria, which switched from Olsenella to Lactobacillus along the pH increase, illustrating the plasticity of the food web in chain elongation communities. Despite long-term cultivation in closed systems over the pH shift experiment, the communities retained functional redundancy in fermentation pathways, reflected by the emergence of rare species and concomitant recovery of chain elongation functions.

TerrestrialMetagenomeDB: a public repository of curated and standardized metadata for terrestrial metagenomes.

Microbiome studies focused on the genetic potential of microbial communities (metagenomics) became standard within microbial ecology. MG-RAST and the Sequence Read Archive (SRA), the two main metagenome repositories, contain over 202 858 public available metagenomes and this number has increased exponentially. However, mining databases can be challenging due to misannotated, misleading and decentralized data. The main goal of TerrestrialMetagenomeDB is to make it easier for scientists to find terrestrial metagenomes of interest that could be compared with novel datasets in meta-analyses. We defined terrestrial metagenomes as those that do not belong to marine environments. Further, we curated the database using text mining to assign potential descriptive keywords that better contextualize environmental aspects of terrestrial metagenomes, such as biomes and materials. TerrestrialMetagenomeDB release 1.0 includes 15 022 terrestrial metagenomes from SRA and MG-RAST. Together, the downloadable data amounts to 68 Tbp. In total, 199 terrestrial terms were divided into 14 categories. These metagenomes span 83 countries, 30 biomes and 7 main source materials. The TerrestrialMetagenomeDB is publicly available at https://webapp.ufz.de/tmdb.

Benzene degradation in a denitrifying biofilm reactor: activity and microbial community composition.

Benzene is an aromatic compound and harmful for the environment. Biodegradation of benzene can reduce the toxicological risk after accidental or controlled release of this chemical in the environment. In this study, we further characterized an anaerobic continuous biofilm culture grown for more than 14 years on benzene with nitrate as electron acceptor. We determined steady state degradation rates, microbial community composition dynamics in the biofilm, and the initial anaerobic benzene degradation reactions. Benzene was degraded at a rate of 0.15 µmol/mg protein/day and a first-order rate constant of 3.04/day which was fourfold higher than rates reported previously. Bacteria belonging to the Peptococcaceae were found to play an important role in this anaerobic benzene-degrading biofilm culture, but also members of the Anaerolineaceae were predicted to be involved in benzene degradation or benzene metabolite degradation based on Illumina MiSeq analysis of 16S ribosomal RNA genes. Biomass retention in the reactor using a filtration finger resulted in reduction of benzene degradation capacity. Detection of the benzene carboxylase encoding gene, abcA, and benzoic acid in the culture vessel indicated that benzene degradation proceeds through an initial carboxylation step.

Competitive inhibition and mutualistic growth in co-infections: deciphering Staphylococcus aureus-Acinetobacter baumannii interaction dynamics.

Staphylococcus aureus (Sa) and Acinetobacter baumannii (Ab) are frequently co-isolated from polymicrobial infections that are severe and refractory to therapy. Here, we apply a combination of wet-lab experiments and in silico modeling to unveil the intricate nature of the Ab/Sa interaction using both, representative laboratory strains and strains co-isolated from clinical samples. This comprehensive methodology allowed uncovering Sa's capability to exert a partial interference on Ab by the expression of phenol-soluble modulins. In addition, we observed a cross-feeding mechanism by which Sa supports the growth of Ab by providing acetoin as an alternative carbon source. This study is the first to dissect the Ab/Sa interaction dynamics wherein competitive and cooperative strategies can intertwine. Through our findings, we illuminate the ecological mechanisms supporting their coexistence in the context of polymicrobial infections. Our research not only enriches our understanding but also opens doors to potential therapeutic avenues in managing these challenging infections.

Evidence for selective bacterial community structuring in the freshwater sponge Ephydatia fluviatilis.

To understand the functioning of sponges, knowledge of the structure of their associated microbial communities is necessary. However, our perception of sponge-associated microbiomes remains mainly restricted to marine ecosystems. Here, we report on the molecular diversity and composition of bacteria in the freshwater sponge Ephydatia fluviatilis inhabiting the artificial lake Vinkeveense Plassen, Utrecht, The Netherlands. Polymerase chain reaction-denaturing gradient gel electrophoresis (PCR-DGGE) fingerprints revealed that the apparent diversities within the domain Bacteria and the phylum Actinobacteria were lower in E. fluviatilis than in bulk water. Enrichment of specific PCR-DGGE bands in E. fluviatilis was detected. Furthermore, sponge- and bulk water-derived bacterial clone libraries differed with respect to bacterial community composition at the phylum level. E. fluviatilis-derived sequences were affiliated with six recognized phyla, i.e., Proteobacteria, Planctomycetes, Actinobacteria, Bacteroidetes, Chlamydiae and Verrucomicrobia, in order of relative abundance; next to the uncultured candidate phylum TM7 and one deeply rooted bacterial lineage of undefined taxonomy (BLUT). Actinobacteria, Proteobacteria, and Bacteroidetes were the dominant bacterial phyla in the freshwater clone library whereas sequences affiliated with Planctomycetes, Verrucomicrobia, Acidobacteria and Armatimonadetes were found at lower frequencies. Fine-tuned phylogenetic inference showed no or negligible overlaps between the E. fluviatilis and water-derived phylotypes within bacterial taxa such as Alphaproteobacteria, Bacteroidetes and Actinobacteria. We also ascertained the status of two alphaproteobacterial lineages as freshwater sponge-specific phylogenetic clusters, and report on high distinctiveness of other E. fluviatilis specific phylotypes, especially within the Bacteroidetes, Planctomycetes and Chlamydia taxa. This study supports the contention that the composition and diversity of bacteria in E. fluviatilis is partially driven by the host organism.

Combining Flow Cytometry and Metagenomics Improves Recovery of Metagenome-Assembled Genomes in a Cell Culture from Activated Sludge.

The recovery of metagenome-assembled genomes is biased towards the most abundant species in a given community. To improve the identification of species, even if only dominant species are recovered, we investigated the integration of flow cytometry cell sorting with bioinformatics tools to recover metagenome-assembled genomes. We used a cell culture of a wastewater microbial community as our model system. Cells were separated based on fluorescence signals via flow cytometry cell sorting into sub-communities: dominant gates, low abundant gates, and outer gates into subsets of the original community. Metagenome sequencing was performed for all groups. The unsorted community was used as control. We recovered a total of 24 metagenome-assembled genomes (MAGs) representing 11 species-level genome operational taxonomic units (gOTUs). In addition, 57 ribosomal operational taxonomic units (rOTUs) affiliated with 29 taxa at species level were reconstructed from metagenomic libraries. Our approach suggests a two-fold increase in the resolution when comparing sorted and unsorted communities. Our results also indicate that species abundance is one determinant of genome recovery from metagenomes as we can recover taxa in the sorted libraries that are not present in the unsorted community. In conclusion, a combination of cell sorting and metagenomics allows the recovery of MAGs undetected without cell sorting.

The fate of sulfonamide resistance genes and anthropogenic pollution marker intI1 after discharge of wastewater into a pristine river stream.

Introduction: Currently there are sparse regulations regarding the discharge of antibiotics from wastewater treatment plants (WWTP) into river systems, making surface waters a latent reservoir for antibiotics and antibiotic resistance genes (ARGs). To better understand factors that influence the fate of ARGs in the environment and to foster surveillance of antibiotic resistance spreading in such habitats, several indicator genes have been proposed, including the integrase gene intI1 and the sulfonamide resistance genes sul1 and sul2. Methods: Here we used quantitative PCR and long-read nanopore sequencing to monitor the abundance of these indicator genes and ARGs present as class 1 integron gene cassettes in a river system from pristine source to WWTP-impacted water. ARG abundance was compared with the dynamics of the microbial communities determined via 16S rRNA gene amplicon sequencing, conventional water parameters and the concentration of sulfamethoxazole (SMX), sulfamethazine (SMZ) and sulfadiazine (SDZ). Results: Our results show that WWTP effluent was the principal source of all three sulfonamides with highest concentrations for SMX (median 8.6 ng/l), and of the indicator genes sul1, sul2 and intI1 with median relative abundance to 16S rRNA gene of 0.55, 0.77 and 0.65%, respectively. Downstream from the WWTP, water quality improved constantly, including lower sulfonamide concentrations, decreasing abundances of sul1 and sul2 and lower numbers and diversity of ARGs in the class 1 integron. The riverine microbial community partially recovered after receiving WWTP effluent, which was consolidated by a microbiome recovery model. Surprisingly, the relative abundance of intI1 increased 3-fold over 13 km of the river stretch, suggesting an internal gene multiplication. Discussion: We found no evidence that low amounts of sulfonamides in the aquatic environment stimulate the maintenance or even spread of corresponding ARGs. Nevertheless, class 1 integrons carrying various ARGs were still present 13 km downstream from the WWTP. Therefore, limiting the release of ARG-harboring microorganisms may be more crucial for restricting the environmental spread of antimicrobial resistance than attenuating ng/L concentrations of antibiotics.

Corrigendum: The fate of sulfonamide resistance genes and anthropogenic pollution marker intI1 after discharge of wastewater into a pristine river stream.

[This corrects the article DOI: 10.3389/fmicb.2023.1058350.].

Improved recovery and annotation of genes in metagenomes through the prediction of fungal introns.

Metagenomics provides a tool to assess the functional potential of environmental and host-associated microbiomes based on the analysis of environmental DNA: assembly, gene prediction and annotation. While gene prediction is straightforward for most bacterial and archaeal taxa, it has limited applicability in the majority of eukaryotic organisms, including fungi that contain introns in gene coding sequences. As a consequence, eukaryotic genes are underrepresented in metagenomics datasets and our understanding of the contribution of fungi and other eukaryotes to microbiome functioning is limited. Here, we developed a machine intelligence-based algorithm that predicts fungal introns in environmental DNA with reasonable precision and used it to improve the annotation of environmental metagenomes. Intron removal increased the number of predicted genes by up to 9.1% and improved the annotation of several others. The proportion of newly predicted genes increased with the share of eukaryotic genes in the metagenome and-within fungal taxa-increased with the number of introns per gene. Our approach provides a tool named SVMmycointron for improved metagenome annotation, especially of microbiomes with a high proportion of eukaryotes. The scripts described in the paper are made publicly available and can be readily utilized by microbiome researchers analysing metagenomics data.

Global Distribution of Carbohydrate Utilization Potential in the Prokaryotic Tree of Life.

Microorganisms dominate all ecosystems on Earth and play a key role in the turnover of organic matter. By producing enzymes, they degrade complex carbohydrates, facilitating the recycling of nutrients and controlling the carbon cycle. Despite their importance, our knowledge regarding microbial carbohydrate utilization has been limited to genome-sequenced taxa and thus heavily biased to specific groups and environments. Here, we used the Genomes from Earth's Microbiomes (GEM) catalog to describe the carbohydrate utilization potential in >7000 bacterial and archaeal taxa originating from a range of terrestrial, marine and host-associated habitats. We show that the production of carbohydrate-active enzymes (CAZymes) is phylogenetically conserved and varies significantly among microbial phyla. High numbers of carbohydrate-active enzymes were recorded in phyla known for their versatile use of carbohydrates, such as Firmicutes, Fibrobacterota, and Armatimonadota, but also phyla without cultured representatives whose carbohydrate utilization potential was so far unknown, such as KSB1, Hydrogenedentota, Sumerlaeota, and UBP3. Carbohydrate utilization potential reflected the specificity of various habitats: the richest complements of CAZymes were observed in MAGs of plant microbiomes, indicating the structural complexity of plant biopolymers. IMPORTANCE This study expanded our knowledge of the phylogenetic distribution of carbohydrate-active enzymes across prokaryotic tree of life, including new phyla where the carbohydrate-active enzymes composition have not been described until now and demonstrated the potential for carbohydrate utilization of numerous yet uncultured phyla. Profiles of carbohydrate-active enzymes are largely habitat-specific and reflect local carbohydrate availability by selecting taxa with appropriate complements of these enzymes. This information should aid in the prediction of functions in microbiomes of known taxonomic composition and helps to identify key components of habitat-specific carbohydrate pools. In addition, these findings have a high relevance for the understanding of carbohydrate utilization and carbon cycling in the environment, the process that is closely link to the carbon storage potential of Earth habitats and the production of greenhouse gasses.

Whole-genome sequence of the filamentous diazotrophic cyanobacterium Tolypothrix sp. PCC 7712 and its comparison with non-diazotrophic Tolypothrix sp. PCC 7601.

Cyanobacteria are highly promising microorganisms in forthcoming biotechnologies. Besides the systematic development of molecular tools for genetic engineering, the design of chassis strains and novel reactor concepts are in focus. The latter includes capillary biofilm reactors (CBR), which offer a high surface area-to-volume ratio and very high cell densities. In this context, Tolypothrix sp. PCC 7712 was found to be highly suited for this reactor system due to maximal surface coverage, extraordinarily strong biofilm attachment, and high biomass formation. Here, we provide the genome sequence of Tolypothrix sp. PCC 7712 to potentially allow targeted strain engineering. Surprisingly, it was almost identical to an available incomplete genome draft of Tolypothrix sp. PCC 7601. Thus, we completely sequenced this strain as well and compared it in detail to strain PCC 7712. Comparative genome analysis revealed 257 and 80 unique protein-coding sequences for strains PCC 7601 and PCC 7712, respectively. Clustering genomes based on average nucleotide identity (ANI) and 16S rRNA homology showed 99.98% similarity and only minor distance, respectively, between the two strains in contrast to 21 other cyanobacterial genomes. Despite these high similarities, both strains differ in the ability to fix atmospheric nitrogen and show specific sequence variations, which are discussed in the paper.

Spatial patterns of microbial diversity in Fe-Mn deposits and associated sediments in the Atlantic and Pacific oceans.

Mining of deep-sea Fe-Mn deposits will remove crusts and nodules from the seafloor. The growth of these minerals takes millions of years, yet little is known about their microbiome. Besides being key elements of the biogeochemical cycles and essential links of food and energy to deep-sea, microbes have been identified to affect manganese oxide formation. In this study, we determined the composition and diversity of Bacteria and Archaea in deep-sea Fe-Mn crusts, nodules, and associated sediments from two areas in the Atlantic Ocean, the Tropic Seamount and the Rio Grande Rise. Samples were collected using ROV and dredge in 2016 and 2018 oceanographic campaigns, and the 16S rRNA gene was sequenced using Illumina platform. Additionally, we compared our results with microbiome data of Fe-Mn crusts, nodules, and sediments from Clarion-Clipperton Zone and Takuyo-Daigo Seamount in the Pacific Ocean. We found that Atlantic seamounts harbor an unusual and unknown Fe-Mn deposit microbiome with lower diversity and richness compared to Pacific areas. Crusts and nodules from Atlantic seamounts have unique taxa (Alteromonadales, Nitrospira, and Magnetospiraceae) and a higher abundance of potential metal-cycling bacteria, such as Betaproteobacteriales and Pseudomonadales. The microbial beta-diversity from Atlantic seamounts was clearly grouped into microhabitats according to sediments, crusts, nodules, and geochemistry. Despite the time scale of million years for these deposits to grow, a combination of environmental settings played a significant role in shaping the microbiome of crusts and nodules. Our results suggest that microbes of Fe-Mn deposits are key in biogeochemical reactions in deep-sea ecosystems. These findings demonstrate the importance of microbial community analysis in environmental baseline studies for areas within the potential of deep-sea mining.

Bacterial communities associated with Chenopodium album and Stellaria media seeds from arable soils.

The bacterial community compositions in Chenopodium album and Stellaria media seeds recovered from soil (soil weed seedbank), from bulk soil, and from seeds harvested from plants grown in the same soils were compared. It was hypothesized that bacterial communities in soil weed seedbanks are distinct from the ones present in bulk soils. For that purpose, bacterial polymerase chain reaction denaturing gradient gel electrophoresis (PCR-DGGE) fingerprints, made from DNA extracts of different soils and seed fractions, were analyzed by principal component analysis. Bacterial fingerprints from C. album and S. media seeds differed from each other and from soil. Further, it revealed that bacterial fingerprints from soil-recovered and plant-harvested seeds from the same species clustered together. Hence, it was concluded that microbial communities associated with seeds in soil mostly originated from the mother plant and not from soil. In addition, the results indicated that the presence of a weed seedbank in arable soils can increase soil microbial diversity. Thus, a change in species composition or size of the soil weed seedbank, for instance, as a result of a change in crop management, could affect soil microbial diversity. The consequence of increased diversity is yet unknown, but by virtue of identification of dominant bands in PCR-DGGE fingerprints as Lysobacter oryzae (among four other species), it became clear that bacteria potentially antagonizing phytopathogens dominate in C. album seeds in soil. The role of these potential antagonists on weed and crop plant growth was discussed.

Temperature management potentially affects carbon mineralization capacity and microbial community composition of a shallow aquifer.

High-temperature aquifer thermal energy storage (HT-ATES) is a promising technique to reduce the CO2 footprint of heat supply in the frame of transitioning to renewable energies. However, HT-ATES causes temperature fluctuations in groundwater ecosystems potentially affecting important microbial-mediated ecosystem services. Hence, assessing the impact of increasing temperatures on the structure and functioning of aquifer microbiomes is crucial to evaluate potential environmental risks associated with HT-ATES. In this study, we investigated the effects of temperature variations (12-80°C) on microbial communities and their capacity to mineralize acetate in aerobically incubated sediment sampled from a pristine aquifer. Compared to natural conditions (12°C), increased acetate mineralization rates were observed at 25°C, 37°C and 45°C, whereas mineralization was decelerated at 60°C and absent at 80°C. Sequencing of 16S rRNA genes revealed that the bacterial diversity in acetate-amended and non-acetate-amended sediments decreased with rising temperatures. Distinct communities dominated by bacterial groups affiliated with meso- and thermophilic bacteria established at 45°C and 60°C, respectively, while the number of archaeal phylotypes decreased. The changes in microbial diversity observed at 45°C and 60°C indicate a potential loss of ecosystem functioning, functional redundancy and resilience, while heat storage at 80°C bears the risk of ecological collapse.

Metagenomes, metatranscriptomes and microbiomes of naturally decomposing deadwood.

Deadwood represents significant carbon (C) stock in a temperate forests. Its decomposition and C mobilization is accomplished by decomposer microorganisms - fungi and bacteria - who also supply the foodweb of commensalist microbes. Due to the ecosystem-level importance of deadwood habitat as a C and nutrient stock with significant nitrogen fixation, the deadwood microbiome composition and function are critical to understanding the microbial processes related to its decomposition. We present a comprehensive suite of data packages obtained through environmental DNA and RNA sequencing from natural deadwood. Data provide a complex picture of the composition and function of microbiome on decomposing trunks of European beech (Fagus sylvatica L.) in a natural forest. Packages include deadwood metagenomes, metatranscriptomes, sequences of total RNA, bacterial genomes resolved from metagenomic data and the 16S rRNA gene and ITS2 metabarcoding markers to characterize the bacterial and fungal communities. This project will be of use to microbiologists, environmental biologists and biogeochemists interested in the microbial processes associated with the transformation of recalcitrant plant biomass.

High biodiversity in a benzene-degrading nitrate-reducing culture is sustained by a few primary consumers.

A key question in microbial ecology is what the driving forces behind the persistence of large biodiversity in natural environments are. We studied a microbial community with more than 100 different types of species which evolved in a 15-years old bioreactor with benzene as the main carbon and energy source and nitrate as the electron acceptor. Using genome-centric metagenomics plus metatranscriptomics, we demonstrate that most of the community members likely feed on metabolic left-overs or on necromass while only a few of them, from families Rhodocyclaceae and Peptococcaceae, are candidates to degrade benzene. We verify with an additional succession experiment using metabolomics and metabarcoding that these few community members are the actual drivers of benzene degradation. As such, we hypothesize that high species richness is maintained and the complexity of a natural community is stabilized in a controlled environment by the interdependencies between the few benzene degraders and the rest of the community members, ultimately resulting in a food web with different trophic levels.

Metagenome-Assembled Genome Sequences of Three Uncultured Planktomarina sp. Strains from the Northeast Atlantic Ocean.

We report three metagenome-assembled genomes (MAGs) of Planktomarina strains from coastal seawater (Portugal) to help illuminate the functions of understudied Rhodobacteraceae bacteria in marine environments. The MAGs encode proteins involved in aerobic anoxygenic photosynthesis and a versatile carbohydrate metabolism, strengthening the role of Planktomarina species in oceanic carbon cycling.

Biotransformation of hexachlorocyclohexanes contaminated biomass for energetic utilization demonstrated in continuous anaerobic digestion system.

Lindane, the γ-hexachlorocyclohexane (HCH) isomer, was among the most used pesticides worldwide. Although it was banned in 2009, residues of Lindane and other HCH-isomers are still found with high concentrations in contaminated fields. For clean-up, phytoremediation combined with anaerobic digestion (AD) of contaminated biomass to produce biogas and fertilizer could be a promising strategy and was tested in two 15 L laboratory-scale continuous stirred tank reactors. During operation over one year by adding HCH isomers (γ, α and ß) consecutively, no negative influence on conventional reactor parameters was observed. The γ- and α-HCH isomers were transformed to chlorobenzene and benzene, and transformation became faster along with time, while ß-HCH was not removed. Genus Methanosaeta and order Clostridiales, showing significant enhancement on abundance with HCH addition, may be used as bioindicators for HCH dehalogenation in AD process. The potential for HCH degradation in AD system was restricted to axial Cl atoms of HCH and it showed slight enantioselective preference towards transformation of (+) α-HCH. Moreover, metabolite benzene was mineralized to CO2 and methane, deducing from tracer experiments with benzene-13C6. Overall, AD appears to be a feasible option for treatment of γ and α-HCHs contaminated biomass.

Endophytic colonization of potato (Solanum tuberosum L.) by a novel competent bacterial endophyte, Pseudomonas putida strain P9, and its effect on associated bacterial communities.

Pseudomonas putida strain P9 is a novel competent endophyte from potato. P9 causes cultivar-dependent suppression of Phytophthora infestans. Colonization of the rhizoplane and endosphere of potato plants by P9 and its rifampin-resistant derivative P9R was studied. The purposes of this work were to follow the fate of P9 inside growing potato plants and to establish its effect on associated microbial communities. The effects of P9 and P9R inoculation were studied in two separate experiments. The roots of transplants of three different cultivars of potato were dipped in suspensions of P9 or P9R cells, and the plants were planted in soil. The fate of both strains was followed by examining colony growth and by performing PCR-denaturing gradient gel electrophoresis (PCR-DGGE). Colonies of both strains were recovered from rhizoplane and endosphere samples of all three cultivars at two growth stages. A conspicuous band, representing P9 and P9R, was found in all Pseudomonas PCR-DGGE fingerprints for treated plants. The numbers of P9R CFU and the P9R-specific band intensities for the different replicate samples were positively correlated, as determined by linear regression analysis. The effects of plant growth stage, genotype, and the presence of P9R on associated microbial communities were examined by multivariate and unweighted-pair group method with arithmetic mean cluster analyses of PCR-DGGE fingerprints. The presence of strain P9R had an effect on bacterial groups identified as Pseudomonas azotoformans, Pseudomonas veronii, and Pseudomonas syringae. In conclusion, strain P9 is an avid colonizer of potato plants, competing with microbial populations indigenous to the potato phytosphere. Bacterization with a biocontrol agent has an important and previously unexplored effect on plant-associated communities.

Mobilisation of bacteria in a fine-grained residual soil by electrophoresis.

An investigation of electrokinetic bacterial mobilisation in a residual soil from gneiss is presented here. The experimental program aimed at assessing the efficacy of electrophoresis against the electro-osmotic flow to transport endospores of Bacillus subtilis LBBMA 155 and nitrogen-starved cells of Pseudomonas sp. LBBMA 81. Electrokinesis was performed on a low hydraulic reconstituted clayey soil column submitted to a 5mA electrical current for 24h. Cells were coccoid-shaped and characterised as possessing low surface hydrophobicity and less than 1microm in diameter. Distribution coefficient for B. subtilis in the soil was between 16.8 and 19.9 times higher than that for Pseudomonas sp. Distribution coefficient for B. subtilis between eluate and anionic exchange column was 11.8 times higher than that for Pseudomonas sp. After the electrokinesis, it was shown that cells and endospores were distributed hyperbolically through the soil probe and moved against the electro-osmotic flow; however, endospores were transported throughout all soil core and starved cells only till half of its length. The higher transport efficiency of B. subtilis endospores was attributed to their higher negative charge on cell surface. These results demonstrate that electrokinesis can be used for bacteria transport in soils with low hydraulic conductivity, even against the electro-osmotic flow.