Applicability of the functional gene catechol 1,2-dioxygenase as a biomarker in the detection of BTEX-degrading Rhodococcus species

Aims: Catechol 1,2-dioxygenase is a key enzyme in the degradation of monoaromatic pollutants. The detection of this gene is in focus today but recently designed degenerate primers are not always suitable. Rhodococcus species are important members of the bacterial community involved in the degradation of aromatic contaminants and their specific detection could help assess functions and activities in the contaminated environments. To reach this aim, specific PCR primer sets were designed for the detection of Rhodococcus related catechol 1,2-dioxygenase genes. Methods and Results: Primers were tested with genetically well-characterized strains isolated in this study and community DNA samples were used as template for Rhodococcus specific PCR as well. The sequences of the catabolic gene in question were subjected to multiple alignment and a phylogenetic tree was created and compared to a 16S rRNA gene based Rhodococcus tree. A strong coherence was observed between the phylogenetic trees. Conclusions: The results strongly support the opinion that there was no recent lateral gene transfer among Rhodococcus species in the case of catechol 1,2-dioxygenase. Significance and Impact of the Study: In gasoline contaminated environments, aromatic hydrocarbon degrading Rhodococcus populations can be identified based upon the detection and sequence analysis of catechol 1,2-dioxygenase gene.     

Taxonomic and functional diversity of atrazine‐degrading bacterial communities enriched from agrochemical factory soil

Aims: To characterize atrazine‐degrading potential of bacterial communities enriched from agrochemical factory soil by analysing diversity and organization of catabolic genes. Methods and Results: The bacterial communities enriched from three different sites of varying atrazine contamination mineralized 65–80% of ¹⁴C ring‐labelled atrazine. The presence of trzN‐atzBC‐trzD, trzN‐atzABC‐trzD and trzN‐atzABCDEF‐trzD gene combinations was determined by PCR. In all enriched communities, trzN‐atzBC genes were located on a 165‐kb plasmid, while atzBC or atzC genes were located on separated plasmids. Quantitative PCR revealed that catabolic genes were present in up to 4% of the community. Restriction analysis of 16S rDNA clone libraries of the three enrichments revealed marked differences in microbial community structure and diversity. Sequencing of selected clones identified members belonging to Proteobacteria (α‐, β‐ and γ‐subclasses), the Actinobacteria, Bacteroidetes and TM7 division. Several 16S rRNA gene sequences were closely related to atrazine‐degrading community members previously isolated from the same contaminated site. Conclusions: The enriched communities represent a complex and diverse bacterial associations displaying heterogeneity of catabolic genes and their functional redundancies at the first steps of the upper and lower atrazine‐catabolic pathway. The presence of catabolic genes in small proportion suggests that only a subset of the community has the capacity to catabolize atrazine. Significance and Impact of the Study: This study provides insights into the genetic specificity and the repertoire of catabolic genes within bacterial communities originating from soils exposed to long‐term contamination by s‐triazine compounds.     

Development of a catabolically significant genetic probe for polycyclic aromatic hydrocarbon-degrading <Emphasis Type="Italic">Mycobacteria</Emphasis> in soil

A gene probe for the detection of polycyclic aromatic hydrocarbon (PAH) induced nidB and nidA dioxygenase genes has been designed from Mycobacteria JLS, KMS, and MCS. The probe detects a catabolic gene involved in the initial steps of PAH biodegradation in mycobacteria. The gene probe is comprised of three PCR primer sets designed to detect the genes that code for two subunits of the PAH induced dioxygenase enzyme within PAH-degrading mycobacteria. The probe was built by combining three primer sets with a DNA extraction procedure that was designed to lyse the gram-positive mycobacteria cells while in the soil matrix and remove PCR inhibitors. The probe was tested on PAH contaminated soils undergoing bioremediation through landfarming and uncontaminated soils from the same site. The PAH gene probe results demonstrate that the dioxygenase genes can be detected in soils. Sequencing the nidA and nidBPCR products verified that the genes were detected in soil. Comparisons of the sequences obtained from the soil probe to seven known nid gene sequences from various PAH-degrading mycobacteria showed between 97 and 99% nucleotide matches with the nidB gene and 95 and 99% matches with the nidA gene.     

Temperature-dependent differences in community structure of bacteria involved in degradation of petroleum hydrocarbons under sulfate-reducing conditions

Aim: The aim of this study was to characterize the microbial community involved in anaerobic degradation of petroleum hydrocarbon under low‐ and moderate‐temperature conditions. Methods and Results: Sulfate‐reducing enrichment cultures growing on crude oil and p‐xylene were established at low and moderate temperatures. Bacterial community structures of the cultures were characterized by 16S rRNA gene‐based analysis and organisms responsible for degradation of p‐xylene were investigated by analysis of the bamA gene, involved in anaerobic degradation of aromatic compounds. The PCR‐denaturing gradient gel electrophoresis analysis indicated significant differences in microbial community structures among the cultures, depending on the temperatures of incubation. Difference depending on the temperatures was also observed in the cloning analysis of the bamA gene performed on the p‐xylene‐degrading enrichment cultures. Majority of clones detected in the culture of moderate temperature were related to Desulfosarcina ovata, whereas more diverse bamA gene sequences were obtained from the culture incubated at low temperature. Conclusions: Temperature‐dependent differences in microbial community were demonstrated by the analyses of two genes. It was suggested that sulfate‐reducing bacteria of phylogenetically different groups might be involved in the degradation of petroleum hydrocarbons in different temperature environments. Significance and Impact of the Study: This study is the first report of p‐xylene‐degrading sulfate‐reducing enrichment culture at low temperature. The results of the experiments at low temperature were distinctly different from those reported in previous studies performed at moderate temperatures.     

The Potential of Bacterial Isolates for Emulsification with a Range of Hydrocarbons

A study was undertaken to investigate the distribution of biosurfactant producing and crude oil degrading bacteria in the oil contaminated environment. This research revealed that hydrocarbon contaminated sites are the potent sources for oil degraders. Among 32 oil degrading bacteria isolated from ten different oil contaminated sites of gasoline and diesel fuel stations, 80% exhibited biosurfactant production. The quantity and emulsification activity of the biosurfactants varied. Pseudomonas sp. DS10‐129 produced a maximum of 7.5 ± 0.4 g/l of biosurfactant with a corresponding reduction in surface tension from 68 mN/m to 29.4 ± 0.7 mN/m at 84 h incubation. The isolates Micrococcus sp. GS2‐22, Bacillus sp. DS6‐86, Corynebacterium sp. GS5‐66, Flavobacterium sp. DS5‐73, Pseudomonas sp. DS10‐129, Pseudomonas sp. DS9‐119 and Acinetobacter sp. DS5‐74 emulsified xylene, benzene, n‐hexane, Bombay High crude oil, kerosene, gasoline, diesel fuel and olive oil. The first five of the above isolates had the highest emulsification activity and crude oil degradation ability and were selected for the preparation of a mixed bacterial consortium, which was also an efficient biosurfactant producing oil emulsifying and degrading culture. During this study, biosurfactant production and emulsification activity were detected in Moraxella sp., Flavobacterium sp. and in a mixed bacterial consortium, which have not been reported before.     

Assessment and modification of degenerate qPCR primers that amplify functional genes from etheneotrophs and vinyl chloride-assimilators

Aims: Degenerate qPCR primer sets that target the functional genes etnC and etnE in etheneotrophs and vinyl chloride‐assimilating bacteria were assessed and modified in an effort to improve performance. Methods and Results: Functional gene abundance in four pure cultures was estimated by qPCR using novel (MRTC and MRTE) and existing (RTC and RTE) degenerate primer sets and compared to abundances estimated with nondegenerate gene‐specific primers (GSPs). Functional gene abundance in groundwater DNA extracted from several contaminated sites was also estimated with MRTC and MRTE primers. Conclusions: MRTC primers displayed significantly improved etnC quantification in both pure cultures and environmental samples. Significance and Impact of the Study: Application of MRTC and MRTE primer sets will enhance microbial ecology studies involving etheneotrophs and qPCR analyses that support vinyl chloride bioremediation strategies.     

Successful phytoremediation of crude-oil contaminated soil at an oil exploration and production company by plants-bacterial synergism

Phytoremediation is a promising approach for the cleanup of soil contaminated with petroleum hydrocarbons. This study aimed to develop plant-bacterial synergism for the successful remediation of crude oil-contaminated soil. A consortia of three endophytic bacteria was augmented to two grasses, Leptochloa fusca and Brachiaria mutica, grown in oil-contaminated soil (46.8 g oil kg^?1 soil) in the vicinity of an oil exploration and production company. Endophytes augmentation improved plant growth, crude oil degradation, and soil health. Maximum oil degradation (80%) was achieved with B. mutica plants augmented with the endophytes and it was significantly (P < 0.05) higher than the use of plants or bacteria individually. Moreover, endophytes showed more persistence, the abundance and expression of alkB gene in the rhizosphere as well as in the endosphere of the tested plants than in unvegetated soil. A positive relationship (r = 0.70) observed between gene expression and crude oil reduction indicates that catabolic gene expression is important for hydrocarbon mineralization. This investigation showed that the use of endophytes with appropriate plant is an effective strategy for the cleanup of oil-contaminated soil under field conditions.     

Metabolic profiles and phylogenetic diversity of microbial communities from chlorinated pesticides contaminated sites of different geographical habitats of India

Aims: To study the microbial communities in three sites contaminated with chlorinated pesticides and evaluation of dehydrodechlorinase (linA) gene variants involved in gamma‐hexachlorocyclohexane (γ‐HCH, lindane) degradation. Methods and Results: Using a culture‐independent method, 16S rRNA genes were amplified from microbial communities occurring in contaminated soils. From 375 clone libraries analysed, 55 different restriction fragment length polymorphism phylotypes were obtained. Dehydrodechlorinase (linA) gene, which initiates the γ‐HCH degradation, was directly amplified by PCR from the DNA extracted from soils. Deduced amino acid sequences of eight variant genotypes of linA showed few amino acid changes. All the variants of linA had mutations of F151L and S154T, and one of the genotype carried 12 amino acid changes when compared to a linA of Sphingomonas sp. reported from the same soil. Conclusions: The microbial communities displayed complex and diverse groups similar to bacteria involved in biodegradation. The presence of biodegradative genes like linA indicates the presence of communities with capacity to biodegrade the persistent pesticide HCH. Significance and Impact of the Study: This study provides insights to evaluate the presence of catabolic genes and assessing the bioremediation potential of the industrial soils contaminated by chlorinated pesticides.     

Novel α‐ketoglutarate dioxygenase tfdA‐related genes are found in soil DNA after exposure to phenoxyalkanoic herbicides

Phenoxyalkanoic herbicides such as 2,4‐dichlorophenoxyacetate (2,4‐D), 2,4‐dichlorophenoxybutyrate (2,4‐DB) or mecoprop are widely used to control broad‐leaf weeds. Several bacteria have been reported to degrade these herbicides using the α‐ketoglutarate‐dependent, 2,4‐dichlorophenoxyacetate dioxygenase encoded by the tfdA gene, as the enzyme catalysing the first step in the catabolic pathway. The effects of exposure to different phenoxyalkanoic herbicides in the soil bacterial community and in the tfdA genes diversity were assessed using an agricultural soil exposed to these anthropogenic compounds. Total community bacterial DNA was analysed by terminal restriction fragment length polymorphism of the 16S rRNA and the tfdA gene markers, and detection and cloning of tfdA gene related sequences, using PCR primer pairs. After up to 4 months of herbicide exposure, significant changes in the bacterial community structure were detected in soil microcosms treated with mecoprop, 2,4‐DB and a mixture of both plus 2,4‐D. An impressive variety of novel tfdA gene related sequences were found in these soil microcosms, which cluster in new tfdA gene related sequence groups, unequally abundant depending on the specific herbicide used in soil treatment. Structural analysis of the putative protein products showed small but significant amino acid differences. These tfdA gene sequence variants are, probably, required for degradation of natural substrate(s) structurally related to these herbicides and their presence explains self‐remediation of soils exposed to phenoxyalkanoic herbicides.     

石油污染土壤自然衰减过程多环芳烃降解基因动态特征

新疆石油污染土壤中微生物多环芳烃(polycyclic aromatic hydrocarbons,PAHs)降解功能基因研究甚少,且环境因子和功能基因之间相关性仍不清楚。【目的】揭示新疆石油污染砂质土壤自然衰减过程中多环芳烃降解关键基因结构和变化规律。【方法】以新疆准东油田为研究区,分析同一采油区不同石油污染年限土壤理化因子和多环芳烃含量变化,采用扩增子测序研究石油自然衰减过程中多环芳烃降解酶基因结构变化规律,利用Mental检验探讨其环境驱动因子。【结果】石油污染时间1年和3年的土壤中有多项理化指标与背景土存在显著性差异,而污染5年土壤与背景土之间仅2项指标具有显著性差异,随石油自然衰减逐渐恢复至正常。石油污染1年的土壤中16种多环芳烃除苊烯和?以外,其余14种多环芳烃均高于石油污染3年和5年土壤,多环芳烃总量和含油率污染1年土壤均显著高于污染3年和5年的土壤,多环芳烃会在污染后短时间内迅速被降解。扩增子测序结果显示,萘双加氧酶基因分类操作单元(operational taxonomic units,OTUs)序列随污染年限延长逐渐增多;芳环羟化双加氧酶基因OTUs序列BLAST(...     

Secondary successional trajectories of structural and catabolic bacterial communities in oil‐polluted soil planted with hybrid poplar

Poplars have widely been used for rhizoremediation of a broad range of organic contaminants for the past two decades. Still, there is a knowledge gap regarding the rhizosphere‐associated bacterial communities of poplars and their dynamics during the remediation process. It is envisaged that a detailed understanding of rhizosphere‐associated microbial populations will greatly contribute to a better design and implementation of rhizoremediation. To investigate the long‐term succession of structural and catabolic bacterial communities in oil‐polluted soil planted with hybrid poplar, we carried out a 2‐year field study. Hybrid aspen (Populus tremula × Populus tremuloides) seedlings were planted in polluted soil excavated from an accidental oil‐spill site. Vegetated and un‐vegetated soil samples were collected for microbial community analyses at seven different time points during the course of 2 years and sampling time points were chosen to cover the seasonal variation in the boreal climate zone. Bacterial community structure was accessed by means of 16S rRNA gene amplicon pyrosequencing, whereas catabolic diversity was monitored by pyrosequencing of alkane hydroxylase and extradiol dioxygenase genes. We observed a clear succession of bacterial communities on both structural and functional levels from early to late‐phase communities. Sphingomonas type extradiol dioxygenases and alkane hydroxylase homologs of Rhodococcus clearly dominated the early‐phase communities. The high‐dominance/low‐diversity functional gene communities underwent a transition to low‐dominance/high‐diversity communities in the late phase. These results pointed towards increased catabolic capacities and a change from specialist to generalist strategy of bacterial communities during the course of secondary succession.     

Induction of aromatic catabolic activity in Sphingomonas aromaticivorans strain F199

Enzyme induction studies with Sphingomonas aromaticivorans F199 demonstrated that both toluene and naphthalene induced expression of both naphthalene and toluene catabolic enzymes. However, neither aromatic compound induced expression of all the enzymes required for complete mineralization of either naphthalene or toluene. Activity measurements in combination with gene sequence analyses indicate that growth on either aromatic substrate in the absence of the other is, therefore, sub-optimal and is predicted to lead to the build-up of metabolites due to imbalance in toluene or naphthalene catabolic enzyme activities. Growth on toluene may be further inhibited by the co-expression of two toluene catabolic pathways, as predicted from gene sequence analyses. One of these pathways may potentially result in the formation of a dead-end intermediate, possibly benzaldehyde. In contrast, either p-cresol or benzoate can support high levels of growth. Analyses of promoter region sequences on the F199 aromatic catabolic plasmid, pNL1, suggest that additional regulatory events are modulated through the interaction of BphR with Sigma54 type promoters and through the binding of a regulator upstream of p-cresol catabolic genes and xylM. We hypothesize that the unusual gene clustering in strain F199 is optimized for simultaneous degradation of multiple aromatic compound classes, possibly in response to the heterogeneous composition of aromatic structures in the fossil organic matter present in the deep Atlantic Coastal Plain sediments from which this bacterium was isolated. Received 26 April 1999/ Accepted in revised form 16 August 1999     

Diversity of 16S rRNA and dioxygenase genes detected in coal‐tar‐contaminated site undergoing active bioremediation

Aims: In order to develop effective bioremediation strategies for polyaromatic hydrocarbons (PAHs) degradation, the composition and metabolic potential of microbial communities need to be better understood, especially in highly PAH contaminated sites in which little information on the cultivation‐independent communities is available. Methods and Results: Coal‐tar‐contaminated soil was collected, which consisted of 122·5 mg g^?1 total extractable PAH compounds. Biodegradation studies with this soil indicated the presence of microbial community that is capable of degrading the model PAH compounds viz naphthalene, phenanthrene and pyrene at 50 ppm each. PCR clone libraries were established from the DNA of the coal‐tar‐contaminated soil, targeting the 16S rRNA to characterize (i) the microbial communities, (ii) partial gene fragment encoding the Rieske iron sulfur center (α‐subunit) common to all PAH dioxygenase enzymes and (iii) β‐subunit of dioxygenase. Phylotypes related to Proteobacteria (Alpha‐, Epsilon‐ and Gammaproteobacteria), Acidobacteria, Actinobacteria, Firmicutes, Gemmatimonadetes and Deinococci were detected in 16S rRNA derived clone libraries. Many of the gene fragment sequences of α‐subunit and β‐subunit of dioxygenase obtained from the respective clone libraries fell into clades that are distinct from the reference dioxygenase gene sequences. Presence of consensus sequence of the Rieske type [2Fe‐2S] cluster binding site suggested that these gene fragments encode for α‐subunit of dioxygenase gene. Conclusions: Sequencing of the cloned libraries representing α‐subunit gene fragments (Rf1) and β‐subunit of dioxygenase showed the presence of hitherto unidentified dioxygenase in coal‐tar‐contaminated soil. Significance and Impact of the Study: The combination of the Rieske primers and bacterial community profiling represents a powerful tool for both assessing bioremediation potential and the exploration of novel dioxygenase genes in a contaminated environment.     

Degradation of crude oil by an arctic microbial consortium

The ability of a psychrotolerant microbial consortium to degrade crude oil at low temperatures was investigated. The enriched arctic microbial community was also tested for its ability to utilize various hydrocarbons, such as long-chain alkanes (n-C₂₄ to n-C₃₄), pristane, (methyl-)naphthalenes, and xylenes, as sole carbon and energy sources. Except for o-xylene and methylnaphthalenes, all tested compounds were metabolized under conditions that are typical for contaminated marine liquid sites, namely at pH 6–9 and at 4–27°C. By applying molecular biological techniques (16S rDNA sequencing, DGGE) nine strains could be identified in the consortium. Five of these strains could be isolated in pure cultures. The involved strains were closely related to the following genera: Pseudoalteromonas (two species), Pseudomonas (two species), Shewanella (two species), Marinobacter (one species), Psychrobacter (one species), and Agreia (one species). Interestingly, the five isolated strains in different combinations were unable to degrade crude oil or its components significantly, indicating the importance of the four unculturable microorganisms in the degradation of single or of complex mixtures of hydrocarbons. The obtained mixed culture showed obvious advantages including stability of the consortium, wide range adaptability for crude oil degradation, and strong degradation ability of crude oil.     

Metabolic networks,microbial ecology and ‘omics’ technologies: towards understanding in situ biodegradation processes

Microbial degradation is the main mechanism responsible for the recovery of contaminated sites, where a huge body of investigations is available in which most concentrate on single isolates from soils capable of mineralizing pollutants. The rapid development of molecular techniques in recent years allows immense insights into the processes in situ, including identification of organisms active in target sites, community member interactions and catabolic gene structures. Only a detailed understanding of the functioning and interactions within microbial communities will allow their rational manipulation for the purpose of optimizing bioremediation efforts. We will present the status of the current capabilities to assess and predict catabolic potential of environmental sites by applying gene fingerprinting, catabolome arrays, metagenomics and complementary ‘omics’ technologies. Collectively, this will allow tracking regulation and evolution within microbial communities ultimately aiming to understand the mechanisms taking place in large scale bioremediation treatments for aromatic decontamination.     

Detection of chlorocatechol 1,2-dioxygenase genes in proteobacteria by PCR and gene probes

In various bacterial strains belonging to the β-subdivision of proteobacteria which are capable of degrading chlorinated monoaromatic compounds, chlorocatechol 1,2-dioxygenase genes were detected by PCR and Southern hybridization. Using PCR primers derived from the conserved sequence motifs of chlorocatechol 1,2-dioxygenase genes tfdC, clcA and tcbC, PCR products of the expected size were obtained with the test strains, but not with negative control strains. The specificity of the PCR products was verified by hybridization using an oligonucleotide probe for an internal sequence motif which is evolutionarily conserved among chlorocatechol 1,2-dioxygenases and some other dioxygenases that catalyze the intradiol aromatic-ring-cleavage. Hybridization with the tfdC PCR product from the 2,4-D degradative plasmid pJP4 under stringent conditions revealed different extents of homology of the chlorocatechol 1,2-dioxygenase genes to the canonical tfdC sequence in the various strains. These findings were confirmed by the nucleotide sequence analysis of the tfdC-specific PCR products. From our results, we conclude that the PCR primer set is more suitable than the hybridization with pJP4-derived gene probes for the detection of diverse chlorocatechol 1,2-dioxygenase genes in proteobacteria.     

Diversity,abundance, and distribution of NO‐forming nitrite reductase–encoding genes in deep‐sea subsurface sediments of the South China Sea

In marine ecosystems, both nitrite‐reducing bacteria and anaerobic ammonium‐oxidizing (anammox) bacteria, containing different types of NO‐forming nitrite reductase–encoding genes, contribute to the nitrogen cycle. The objectives of study were to reveal the diversity, abundance, and distribution of NO‐forming nitrite reductase–encoding genes in deep‐sea subsurface environments. Results showed that higher diversity and abundance of nirS gene than nirK and Scalindua‐nirS genes were evident in the sediments of the South China Sea (SCS), indicating bacteria containing nirS gene dominated the NO‐forming nitrite‐reducing microbial community in this ecosystem. Similar diversity and abundance distribution patterns of both nirS and Scalindua‐nirS genes were detected in this study sites, but different from nirK gene. Further statistical analyses also showed both nirS and Scalindua‐nirS genes respond similarly to environmental factors, but differed from nirK gene. These results suggest that bacteria containing nirS and Scalindua‐nirS genes share similar niche in deep‐sea subsurface sediments of the SCS, but differed from those containing nirK gene, indicating that community structures of nitrite‐reducing bacteria are segregated by the functional modules (NirS vs. NirK) rather than the competing processes (anammox vs. classical denitrification).     

Physiological aspects of hydrocarbon emulsification, metal resistance and DNA profile of biodegrading bacteria isolated from oil polluted sites

The production of biosurfactants was evaluated for seven bacterial strains isolated from different oil contaminated sites by the Emulsification Index using diesel oil as the hydrocarbon source. Minimum Inhibitory Concentrations of Mg²⁺, Cr³⁺ and Cu²⁺ were determined to identify the less sensitive bacteria in order to select the best strains for bioremediation. Plasmid extraction was also performed in order to search for gene sequences involved with biosurfactant synthesis. All strains were able to emulsify diesel oil. Rhodococcus ruber AC239 presented the best index (58%), followed by other Rhodococcus strains. Pseudomonas aeruginosa, R. ruber AC239, AC87 and R. erytropolis AC272 presented smallest sensitivities to heavy metals used, being suitable for use in sites contaminated with high concentrations of them. No plasmid DNA was detected showing that biosurfactant coding genes should be in the chromosomal DNA.     

Fungal community diversity and soil health in intensive potato cropping systems of the east Po valley, northern Italy

An ecological approach was used to investigate the relationship between diversity of soil fungal communities and soil‐borne pathogen inoculum in a potato growing area of northern Italy affected by yield decline. The study was performed in 14 sites with the same tillage management practices: 10 named ‘potato sites’, that for many years had been intensely cultivated with potatoes, and 4 named ‘rotation sites’, subject to a 4‐year rotation without potatoes or any recurrent crop for many years. Fungal communities were recorded using conventional (soil fungi by plate count and endophytic fungi as infection frequency on pot‐grown potato plant roots in soil samples) and molecular approaches [Basidiomycetes and Ascomycetes with specific and denaturing gradient gel electrophoresis (DGGE) analysis]. Diversity of fungal communities in potato sites was significantly lower than that in rotation sites. In addition, fungal communities in rotation sites showed lower Berger–Parker dominance than those in the potato sites, suggesting that rotation sites had a higher diversity as well as a better fungal community balance than potato sites. The ANalysis Of SIMilarity test of soil fungi and root endophytic fungi revealed that the two cropping systems differed significantly for species composition. Root endophytic fungal communities showed a greater ability to colonise potato roots in soil samples from potato sites than those from rotation sites. Moreover, the majority of endophytic root fungal community species in potato sites belonged to the potato root rot complex and storage disease (Colletotrichum coccodes, Fusarium solani and Fusarium oxysporum), while those in rotation sites were mainly ubiquitous or saprobic fungi. Soil rDNA analyses showed that Ascomycetes were much more frequent than Basidiomycetes in all the soils examined. DGGE analysis, with the Ascomycete‐specific primer (ITS1F/ITS4A), did not reveal distinctions between the communities found at the potato and rotation sites, although the same analysis showed differences between the communities of Basidiomycetes (specific primer ITS1F/ITS4B). These findings showed that recurrent potato cropping affected diversity and composition of soil fungal communities and induced a shift in specialisation of the endophytic fungi towards potato.