Differential responses of soil microbial biomass, diversity and interactions to land use intensity at a territorial scale

Impact of land use intensification on soil microbial communities across a territory remains poorly documented. Yet, it has to be deciphered to validate the results obtained at local and global scales by integrating the variations of environmental conditions and agricultural systems at a territorial scale. We investigated the impact of different land uses (from forest to agricultural systems) and associated soil management practices on soil molecular microbial biomass and diversity across a territory of 3300 km2 in Burgundy (France). Microbial biomass and diversity were determined by quantifying and high-throughput sequencing of soil DNA from 300 soils, respectively. Geostatistics were applied to map the soil macro-ecological patterns and variance partitioning analysis was used to rank the influence of soil physicochemical characteristics, land uses and associated practices on soil microbial communities. Geographical patterns differed between microbial biomass and diversity, emphasizing that distinct environmental drivers shaped these parameters. Soil microbial biomass was mainly driven by the soil organic carbon content and was significantly altered by agricultural land uses, with a loss of about 71 % from natural to agricultural ecosystems. The best predictors of bacterial and fungal richness were soil texture and pH, respectively. Microbial diversity was less sensitive than microbial biomass to land use intensification, and fungal richness appeared more impacted than bacteria. Co-occurrence network analysis of the interactions among microbial communities showed a decline of about 95 % of network complexity with land use intensification, which counterbalanced the weak response of microbial diversity. Grouping of the 147 cropland plots in four clusters according to their agricultural practices confirmed that microbial parameters exhibited different responses to soil management intensification, especially soil tillage and crop protection. Our results altogether allow evaluating the different levels of microbial parameters' vulnerability to land use intensity at a territorial scale.

Soil bacterial community composition is more stable in kiwifruit orchards relative to phyllosphere communities over time

BACKGROUND

Soil and phyllosphere (leaves and fruit) microbes play critical roles in the productivity and health of crops. However, microbial community dynamics are currently understudied in orchards, with a limited number incorporating temporal monitoring. We used 16S rRNA gene amplicon sequencing to investigate bacterial community temporal dynamics and community assembly processes on the leaves and fruit, and in the soil of 12 kiwifruit orchards across a cropping season in New Zealand.

RESULTS

Community composition significantly differed (P < 0.001) among the three sample types. However, the communities in the phyllosphere substrates more closely resembled each other, relative to the communities in the soil. There was more temporal stability in the soil bacterial community composition, relative to the communities residing on the leaves and fruit, and low similarity between the belowground and aboveground communities. Bacteria in the soil were more influenced by deterministic processes, while stochastic processes were more important for community assembly in the phyllosphere.

CONCLUSIONS

The higher temporal variability and the stochastic nature of the community assembly processes observed in the phyllosphere communities highlights why predicting the responsiveness of phyllosphere communities to environmental change, or the likelihood of pathogen invasion, can be challenging. The relative temporal stability and the influence of deterministic selection on soil microbial communities suggests a greater potential for their prediction and reliable manipulation.

Population genomics of a predatory mammal reveals patterns of decline and impacts of exposure to toxic toads

Mammal declines across northern Australia are one of the major biodiversity loss events occurring globally. There has been no regional assessment of the implications of these species declines for genomic diversity. To address this, we conducted a species-wide assessment of genomic diversity in the northern quoll (Dasyurus hallucatus), an Endangered marsupial carnivore. We used next generation sequencing methods to genotype 10,191 single nucleotide polymorphisms (SNPs) in 352 individuals from across a 3220-km length of the continent, investigating patterns of population genomic structure and diversity, and identifying loci showing signals of putative selection. We found strong heterogeneity in the distribution of genomic diversity across the continent, characterized by (i) biogeographical barriers driving hierarchical population structure through long-term isolation, and (ii) severe reductions in diversity resulting from population declines, exacerbated by the spread of introduced toxic cane toads (Rhinella marina). These results warn of a large ongoing loss of genomic diversity and associated adaptive capacity as mammals decline across northern Australia. Encouragingly, populations of the northern quoll established on toad-free islands by translocations appear to have maintained most of the initial genomic diversity after 16 years. By mapping patterns of genomic diversity within and among populations, and investigating these patterns in the context of population declines, we can provide conservation managers with data critical to informed decision-making. This includes the identification of populations that are candidates for genetic management, the importance of remnant island and insurance/translocated populations for the conservation of genetic diversity, and the characterization of putative evolutionarily significant units.

pgHMA: Application of the heteroduplex mobility assay analysis in phylogenetics and population genetics

The heteroduplex mobility assay (HMA) has proven to be a robust tool for the detection of genetic variation. Here, we describe a simple and rapid application of the HMA by microfluidic capillary electrophoresis, for phylogenetics and population genetic analyses (pgHMA). We show how commonly applied techniques in phylogenetics and population genetics have equivalents with pgHMA: phylogenetic reconstruction with bootstrapping, skyline plots, and mismatch distribution analysis. We assess the performance and accuracy of pgHMA by comparing the results obtained against those obtained using standard methods of analyses applied to sequencing data. The resulting comparisons demonstrate that: (a) there is a significant linear relationship (R²  = .992) between heteroduplex mobility and genetic distance, (b) phylogenetic trees obtained by HMA and nucleotide sequences present nearly identical topologies, (c) clades with high pgHMA parametric bootstrap support also have high bootstrap support on nucleotide phylogenies, (d) skyline plots estimated from the UPGMA trees of HMA and Bayesian trees of nucleotide data reveal similar trends, especially for the median trend estimate of effective population size, and (e) optimized mismatch distributions of HMA are closely fitted to the mismatch distributions of nucleotide sequences. In summary, pgHMA is an easily-applied method for approximating phylogenetic diversity and population trends.

An assembly-free method of phylogeny reconstruction using short-read sequences from pooled samples without barcodes

A current strategy for obtaining haplotype information from several individuals involves short-read sequencing of pooled amplicons, where fragments from each individual is identified by a unique DNA barcode. In this paper, we report a new method to recover the phylogeny of haplotypes from short-read sequences obtained using pooled amplicons from a mixture of individuals, without barcoding. The method, AFPhyloMix, accepts an alignment of the mixture of reads against a reference sequence, obtains the single-nucleotide-polymorphisms (SNP) patterns along the alignment, and constructs the phylogenetic tree according to the SNP patterns. AFPhyloMix adopts a Bayesian inference model to estimate the phylogeny of the haplotypes and their relative abundances, given that the number of haplotypes is known. In our simulations, AFPhyloMix achieved at least 80% accuracy at recovering the phylogenies and relative abundances of the constituent haplotypes, for mixtures with up to 15 haplotypes. AFPhyloMix also worked well on a real data set of kangaroo mitochondrial DNA sequences.

In evolutionary studies, it is customary to obtain homologous sequences from different individuals in a population or a species to construct a phylogeny. Frequently, sequences from different individuals will be identical; we refer to a set of identical sequences as a haplotype. If short-read sequencing technologies are used to obtain sequences from many individuals, the sequence from each individual is tagged with a unique barcode, and a mixed sample of tagged sequences is subsequently sequenced. The tagged sequences can be identified using the appropriate bioinformatics tools, for further downstream analyses. We have developed a novel method, AFPhyloMix, to reconstruct the phylogeny of a mixed sample of homologous sequences, and the relative abundance of different haplotypes, from different individuals without the need for barcoding. AFPhyloMix aligns the short reads obtained to a reference alignment, and identifies the variable sites along the alignment. On the basis of the patterns of nucleotide frequencies at these and neighbouring sites, AFPhyloMix uses a Bayesian inference model to compute the phylogenetic tree and the haplotype relative abundances. Our results show that AFPhyloMix works well on both the simulated data set and the real data set.

Loss of vocal culture and fitness costs in a critically endangered songbird

Cultures in humans and other species are maintained through interactions among conspecifics. Declines in population density could be exacerbated by culture loss, thereby linking culture to conservation. We combined historical recordings, citizen science and breeding data to assess the impact of severe population decline on song culture, song complexity and individual fitness in critically endangered regent honeyeaters (Anthochaera phrygia). Song production in the remaining wild males varied dramatically, with 27% singing songs that differed from the regional cultural norm. Twelve per cent of males, occurring in areas of particularly low population density, completely failed to sing any species-specific songs and instead sang other species' songs. Atypical song production was associated with reduced individual fitness, as males singing atypical songs were less likely to pair or nest than males that sang the regional cultural norm. Songs of captive-bred birds differed from those of all wild birds. The complexity of regent honeyeater songs has also declined over recent decades. We therefore provide rare evidence that a severe decline in population density is associated with the loss of vocal culture in a wild animal, with concomitant fitness costs for remaining individuals. The loss of culture may be a precursor to extinction in declining populations that learn selected behaviours from conspecifics, and therefore provides a useful conservation indicator.

Effective machine-learning assembly for next-generation amplicon sequencing with very low coverage

BACKGROUND

In short-read DNA sequencing experiments, the read coverage is a key parameter to successfully assemble the reads and reconstruct the sequence of the input DNA. When coverage is very low, the original sequence reconstruction from the reads can be difficult because of the occurrence of uncovered gaps. Reference guided assembly can then improve these assemblies. However, when the available reference is phylogenetically distant from the sequencing reads, the mapping rate of the reads can be extremely low. Some recent improvements in read mapping approaches aim at modifying the reference according to the reads dynamically. Such approaches can significantly improve the alignment rate of the reads onto distant references but the processing of insertions and deletions remains challenging.

RESULTS

Here, we introduce a new algorithm to update the reference sequence according to previously aligned reads. Substitutions, insertions and deletions are performed in the reference sequence dynamically. We evaluate this approach to assemble a western-grey kangaroo mitochondrial amplicon. Our results show that more reads can be aligned and that this method produces assemblies of length comparable to the truth while limiting error rate when classic approaches fail to recover the correct length. Finally, we discuss how the core algorithm of this method could be improved and combined with other approaches to analyse larger genomic sequences.

CONCLUSIONS

We introduced an algorithm to perform dynamic alignment of reads on a distant reference. We showed that such approach can improve the reconstruction of an amplicon compared to classically used bioinformatic pipelines. Although not portable to genomic scale in the current form, we suggested several improvements to be investigated to make this method more flexible and allow dynamic alignment to be used for large genome assemblies.

Assemblage of Focal Species Recognizers-AFSR: A technique for decreasing false indications of presence from acoustic automatic identification in a multiple species context

Passive acoustic monitoring (PAM) coupled with automated species identification is a promising tool for species monitoring and conservation worldwide. However, high false indications of presence are still an important limitation and a crucial factor for acceptance of these techniques in wildlife surveys. Here we present the Assemblage of Focal Species Recognizers—AFSR, a novel approach for decreasing false positives and increasing models’ precision in multispecies contexts. AFSR focusses on decreasing false positives by excluding unreliable sound file segments that are prone to misidentification. We used MatlabHTK, a hidden Markov models interface for bioacoustics analyses, for illustrating AFSR technique by comparing two approaches, 1) a multispecies recognizer where all species are identified simultaneously, and 2) an assemblage of focal species recognizers (AFSR), where several recognizers that each prioritise a single focal species are then summarised into a single output, according to a set of rules designed to exclude unreliable segments. Both approaches (the multispecies recognizer and AFSR) used the same sound files training dataset, but different processing workflow. We applied these recognisers to PAM recordings from a remote island colony with five seabird species and compared their outputs with manual species identifications. False positives and precision improved for all the five species when using AFSR, achieving remarkable 0% false positives and 100% precision for three of five seabird species, and < 6% false positives, and >90% precision for the other two species. AFSR’ output was also used to generate daily calling activity patterns for each species. Instead of attempting to withdraw useful information from every fragment in a sound recording, AFSR prioritises more trustworthy information from sections with better quality data. AFSR can be applied to automated species identification from multispecies PAM recordings worldwide.

Genomic impact of severe population decline in a nomadic songbird

Uncovering the population genetic histories of non-model organisms is increasingly possible through advances in next generation sequencing and DNA sampling of museum specimens. This new information can inform conservation of threatened species, particularly those for which historical and contemporary population data are unavailable or challenging to obtain. The critically endangered, nomadic regent honeyeater Anthochaera phrygia was abundant and widespread throughout south-eastern Australia prior to a rapid population decline and range contraction since the 1970s. A current estimated population of 250-400 individuals is distributed sparsely across 600,000 km2 from northern Victoria to southern Queensland. Using hybridization RAD (hyRAD) techniques, we obtained a SNP dataset from 64 museum specimens (date 1879-1960), 102 'recent' (1989-2012) and 52 'current' (2015-2016) wild birds sampled throughout the historical and contemporary range. We aimed to estimate population genetic structure, genetic diversity and population size of the regent honeyeater prior to its rapid decline. We then assessed the impact of the decline on recent and current population size, structure and genetic diversity. Museum sampling showed population structure in regent honeyeaters was historically low, which remains the case despite a severe fragmentation of the breeding range. Population decline has led to minimal loss of genetic diversity since the 1980's. Capacity to quantify the overall magnitude of both genetic diversity loss and population decline was limited by the poorer quality of genomic data derived from museum specimens. A rapid population decline, coupled with the regent honeyeater's high mobility, means a detectable genomic impact of this decline has not yet manifested. Extinction may occur in this nomadic species before a detectable genomic impact of small population size is realised. We discuss the implications for genetic management of endangered mobile species and enhancing the value of museum specimens in population genomic studies.

Multi-locus DNA metabarcoding of zooplankton communities and scat reveal trophic interactions of a generalist predator

To understand the ecosystem dynamics that underpin the year-round presence of a large generalist consumer, the Bryde's whale (Balaenoptera edeni brydei), we use a DNA metabarcoding approach and systematic zooplankton surveys to investigate seasonal and regional changes in zooplankton communities and if whale diet reflects such changes. Twenty-four zooplankton community samples were collected from three regions throughout the Hauraki Gulf, New Zealand, over two temperature regimes (warm and cool seasons), as well as 20 samples of opportunistically collected Bryde's whale scat. Multi-locus DNA barcode libraries were constructed from 18S and COI gene fragments, representing a trade-off between identification and resolution of metazoan taxa. Zooplankton community OTU occurrence and relative read abundance showed regional and seasonal differences based on permutational analyses of variance in both DNA barcodes, with significant changes in biodiversity indices linked to season in COI only. In contrast, we did not find evidence that Bryde's whale diet shows seasonal or regional trends, but instead indicated clear prey preferences for krill-like crustaceans, copepods, salps and ray-finned fishes independent of prey availability. The year-round presence of Bryde's whales in the Hauraki Gulf is likely associated with the patterns of distribution and abundance of these key prey items.

HaploJuice : accurate haplotype assembly from a pool of sequences with known relative concentrations

Background

Pooling techniques, where multiple sub-samples are mixed in a single sample, are widely used to take full advantage of high-throughput DNA sequencing. Recently, Ranjard et al. (PLoS ONE 13:0195090, 2018) proposed a pooling strategy without the use of barcodes. Three sub-samples were mixed in different known proportions (i.e. 62.5%, 25% and 12.5%), and a method was developed to use these proportions to reconstruct the three haplotypes effectively.

Results

HaploJuice provides an alternative haplotype reconstruction algorithm for Ranjard et al.’s pooling strategy. HaploJuice significantly increases the accuracy by first identifying the empirical proportions of the three mixed sub-samples and then assembling the haplotypes using a dynamic programming approach. HaploJuice was evaluated against five different assembly algorithms, Hmmfreq (Ranjard et al., PLoS ONE 13:0195090, 2018), ShoRAH (Zagordi et al., BMC Bioinformatics 12:119, 2011), SAVAGE (Baaijens et al., Genome Res 27:835-848, 2017), PredictHaplo (Prabhakaran et al., IEEE/ACM Trans Comput Biol Bioinform 11:182-91, 2014) and QuRe (Prosperi and Salemi, Bioinformatics 28:132-3, 2012). Using simulated and real data sets, HaploJuice reconstructed the true sequences with the highest coverage and the lowest error rate.

Conclusion

HaploJuice provides high accuracy in haplotype reconstruction, making Ranjard et al.’s pooling strategy more efficient, feasible, and applicable, with the benefit of reducing the sequencing cost.

Reassembling haplotypes in a mixture of pooled amplicons when the relative concentrations are known: A proof-of-concept study on the efficient design of next-generation sequencing strategies

Next-generation sequencing can be costly and labour intensive. Usually, the sequencing cost per sample is reduced by pooling amplified DNA = amplicons) derived from different individuals on the same sequencing lane. Barcodes unique to each amplicon permit short-read sequences to be assigned appropriately. However, the cost of the library preparation increases with the number of barcodes used. We propose an alternative to barcoding: by using different known proportions of individually-derived amplicons in a pooled sample, each is characterised a priori by an expected depth of coverage. We have developed a Hidden Markov Model that uses these expected proportions to reconstruct the input sequences. We apply this method to pools of mitochondrial DNA amplicons extracted from kangaroo meat, genus Macropus. Our experiments indicate that the sequence coverage can be efficiently used to index the short-reads and that we can reassemble the input haplotypes when secondary factors impacting the coverage are controlled. We therefore demonstrate that, by combining our approach with standard barcoding, the cost of the library preparation is reduced to a third.

Visualization and Quantification of Mesenchymal Cell Adipogenic Differentiation Potential with a Lineage Specific Marker

Several dyes are currently available for use in detecting differentiation of mesenchymal cells into adipocytes. Dyes, such as Oil Red O, are cheap, easy to use and widely utilized by laboratories analyzing the adipogenic potential of mesenchymal cells. However, they are not specific to changes in gene transcription. We have developed a gene-specific differentiation assay to analyze when a mesenchymal cell has switched its fate to an adipogenic lineage. Immuno-labelling against fatty acid binding protein-4 (FABP4), a lineage-specific marker of adipogenic differentiation, enabled visualization and quantification of differentiated cells. The ability to quantify adipogenic differentiation potential of mesenchymal cells in a 96 well microplate format has promising implications for a number of applications. Hundreds of clinical trials involve the use of adult mesenchymal stromal cells and it is currently difficult to correlate therapeutic outcomes within and especially between such clinical trials. This simple high-throughput FABP4 assay provides a quantitative assay for assessing the differentiation potential of patient-derived cells and is a robust tool for comparing different isolation and expansion methods. This is particularly important given the increasing recognition of the heterogeneity of the cells being administered to patients in mesenchymal cell products. The assay also has potential utility in high throughput drug screening, particularly in obesity and pre-diabetes research.

Complete mitochondrial genome of the green-lipped mussel, Perna canaliculus (Mollusca: Mytiloidea), from long nanopore sequencing reads

We describe here the first complete genome assembly of the New Zealand green-lipped mussel, Perna canaliculus, mitochondrion. The assembly was performed de novo from a mix of long nanopore sequencing reads and short sequencing reads. The genome is 16,005 bp long. Comparison to other Mytiloidea mitochondrial genomes indicates important gene rearrangements in this family.

Integration over song classification replicates: song variant analysis in the hihi

Human expert analyses are commonly used in bioacoustic studies and can potentially limit the reproducibility of these results. In this paper, a machine learning method is presented to statistically classify avian vocalizations. Automated approaches were applied to isolate bird songs from long field recordings, assess song similarities, and classify songs into distinct variants. Because no positive controls were available to assess the true classification of variants, multiple replicates of automatic classification of song variants were analyzed to investigate clustering uncertainty. The automatic classifications were more similar to the expert classifications than expected by chance. Application of these methods demonstrated the presence of discrete song variants in an island population of the New Zealand hihi (Notiomystis cincta). The geographic patterns of song variation were then revealed by integrating over classification replicates. Because this automated approach considers variation in song variant classification, it reduces potential human bias and facilitates the reproducibility of the results.

Analyses of sex and individual differences in vocalizations of Australasian gannets using a dynamic time warping algorithm

The study of the evolution of sexual differences in behavioral and morphological displays requires analyses of the extent of sexual dimorphism across various sensory modalities. In the seabird family Sulidae, boobies show dramatic sexual dimorphism in their vocalizations, and gannet calls have also been suggested to be dimorphic to human observers. This study aimed to evaluate the presence of sexually dimorphic calls in the Australasian gannet (Morus serrator) through the first comprehensive description of its vocalizations recorded at two localities; Cape Kidnappers, where individuals were banded and sexed from DNA samples, and at the Muriwai gannetry, both on the North Island of New Zealand. Calls were first inspected using basic bioacoustic features to establish a library of call element types for general reference. Extensive multivariate tests, based on a dynamic time warping algorithm, subsequently revealed that no sexual differences could be detected in Australasian gannet calls. The analyses, however, indicated extensive and consistent vocal variation between individuals, particularly so in female gannets, which may serve to signal individual identity to conspecifics. This study generates predictions to identify whether differences in Australasian gannet vocalizations play perceptual and functional roles in the breeding and social biology of this long-lived biparental seabird species.

Contamination of soil by copper affects the dynamics, diversity, and activity of soil bacterial communities involved in wheat decomposition and carbon storage

A soil microcosm experiment was conducted to evaluate the influence of copper contamination on the dynamics and diversity of bacterial communities actively involved in wheat residue decomposition. In the presence of copper, a higher level of CO(2) release was observed, which did not arise from greater wheat decomposition but from a higher level of stimulation of soil organic matter mineralization (known as the priming effect). Such functional modifications may be related to significant modifications in the diversity of active bacterial populations characterized using the DNA stable-isotope probing approach.

Unsupervised bird song syllable classification using evolving neural networks

Evolution of bird vocalizations is subjected to selection pressure related to their functions. Passerine bird songs are also under a neutral model of evolution because of the learning process supporting their transmission; thus they contain signals of individual, population, and species relationships. In order to retrieve this information, large amounts of data need to be processed. From vocalization recordings, songs are extracted and encoded as sequences of syllables before being compared. Encoding songs in such a way can be done either by ear and spectrogram visual analysis or by specific algorithms permitting reproducible studies. Here, a specific automatic method is presented to compute a syllable distance measure allowing an unsupervised classification of song syllables. Results obtained from the encoding of White-crowned Sparrow (Zonotrichia leucophrys pugetensis) songs are compared to human-based analysis.

Distribution and genetic diversity of bacterial thiopurine methyltransferases in soils emitting dimethyl selenide

Dimethyl selenide (DMSe) and dimethyl diselenide (DMDSe) emissions by soil samples spiked with selenite or (methyl)selenocysteine, with or without a supplement of nutrient broth and glucose were measured. DMSe was the main form of volatile Se produced, and was observed for both Se-substrates. DMDSe was only emitted from soils spiked with (methyl)selenocysteine. Two bacterial thiopurine methyltransferases (TPMTs), TPMT-I and TPMT-E, have been reported to be involved in DMSe and DMDSe emissions [J. Bacteriol. 184 (2002) 3146; Appl. Environ. Microbiol. 69 (2003) 3784]. To establish if these TPMTs or other members of their gene family could have contributed to the DMSe emissions observed, the diversity of bTPMT gene (tpm) sequences among the soils of this study was investigated. Total DNAs from these soils were extracted and screened using the tpm PTCF2-PTCR2 consensus primers defined to PCR amplify this gene family. The PCR products obtained from two soils were cloned, analysed by PCR-RFLP, and sequenced. Their analysis showed an important diversity of tpm lineages (around 12) in soils. Phylogenetic analysis of the deduced TPMT sequences of these soils revealed lineages not previously recorded in the databases, sequences closely related or identical to freshwater TPMTs, or sequences encoding TPMTs closely related to those of Pseudomonas fragi TPMT-K, Pseudomonas Hsa.28 TPMT-I, or Colwellia psychrerythraea TPMT-Z. Nested PCRs, allowing detection of about 13 distinct tpm soil and freshwater lineages by PTCF2-PTCR2 PCR screenings, were performed on the soil total DNAs. These PCRs confirmed the sequencing data, and allowed to recover lineages not detected by the cloning strategy. These results indicate that soils, like the freshwater samples, harbour TPMT-I gene sequences but may also have distinct tpm lineages. This study further supports our hypothesis that TPMTs contribute to DMSe soil emissions.

Cumulative effects of short-term polymetal contamination on soil bacterial community structure

In this study we evaluated the short-term effects of copper, cadmium, and mercury, added singly or in combination at different doses, on soil bacterial community structure using the bacterial automated ribosomal intergenic spacer analysis (B-ARISA) fingerprinting technique. Principal-component analysis of B-ARISA profiles allowed us to deduce the following order of impact: (Cu + Cd + Hg) >> Hg > or = Cd > Cu. These results demonstrated that there was a cumulative effect of metal toxicity. Furthermore, the trend of modifications was consistent with the "hump-backed" relationships between biological diversity and disturbance described by Giller et al. (K. E. Giller, E. Witler, and S. P. McGrath, Soil Biol. Biochem. 30:1389-1414, 1998).

Dynamic of the genetic structure of bacterial and fungal communities at different developmental stages of Medicago truncatula Gaertn. cv. Jemalong line J5

The genetic structure of bacterial and fungal communities was characterized in the rhizosphere of Medicago truncatula Gaertn. cv. Jemalong line J5 at five developmental stages (three vegetative and two reproductive stages), and in three compartments (bulk soil, rhizosphere soil and root tissues). The genetic structure of microbial communities was determined by cultivation-independent methods using directly extracted DNA that was characterized by automated ribosomal intergenic spacer analysis (ARISA). Principal component analyses (PCA) indicate that, for all developmental stages, the genetic structure of microbial communities differed significantly by compartment, with a major shift in the community in root tissues corresponding to the most intimate compartment with the plant. Differences were also recorded during plant development, the most significant being observed during the transition between vegetative and reproductive stages. Throughout this period, plants were shown to establish the highest level of symbiotic association (mycorrhization, nodulation) with arbuscular mycorrhizal fungi and Rhizobia. During the reproductive stages, the dynamics of the genetic structure differed between bacterial and fungal communities. At the last reproductive stage, the genetic structure of bacterial communities became close to that recorded during the first vegetative stages, suggesting a resilience phenomenon, whereas the genetic structure of fungal communities remained different from the vegetative stages and also from the early reproductive stages, suggesting a persistence of the rhizosphere effect.

Freshwater selenium-methylating bacterial thiopurine methyltransferases: diversity and molecular phylogeny

The diversity of bacterial thiopurine methyltransferases (bTPMT) among five natural Se-methylating freshwaters was investigated by polymerase chain reaction (PCR) screenings and sequencings. DNA sequence analyses confirmed the cloned products' identity and revealed a broad diversity of freshwater TPMTs. Neighbour-joining (NJ) phylogenetic analyses combining these sequences, all GenBank entries closely related to these sequences and deduced TPMTs obtained in this work from selected gamma-proteobacteria showed TPMTs to form a distinct radiation, closely related to UbiG methyltransferases. Inside the TPMT phylogenetic cluster, eukaryote sequences diverged early from the bacterial ones, and all the bacterial database entries belonged to a subgroup of gamma-proteobacteria, with an apparent lateral transfer of a particular allele to beta-proteobacteria of Bordetella. The NJ phylogenetic tree revealed 22 bTPMT lineages, 10 of which harboured freshwater sequences. All lineages showed deep and long branches indicative of major genetic drifts outside regions encoding highly conserved domains. Selected residues among these highly variable domains could reflect adaptations for particular ecological niches. PCR lineage-specific primers differentiated Se-methylating freshwaters according to their 'tpm lineage' signatures. Most freshwater tpm alleles were found to be distinct from those available in the databases, but a group of tpm was found encoding TPMTs identical to an Aeromonas veronii TPMT characterized in this work.

Shifts in diversity and microscale distribution of the adapted bacterial phenotypes due to Hg(II) spiking in soil

In a previous experiment [Ranjard et al. (2000) FEMS Microbiol Ecol 31:107-115], the spatial heterogeneity of a mercury impact on soil bacterial community was revealed by an increase of mercury-resistant (HgR) bacterial numbers in the outer fraction and the sand fractions when compared to those in the silt fractions. The objectives of the present study were (i) to investigate whether mercury exposure affects the diversity and the distribution within the various fractions of the HgR populations and (ii) to evaluate the contribution of the HgR populations to the overall community adaptation. A total of 236 strains isolated before (104 isolates) and 30 days (132 isolates) after spiking were characterized by an amplified ribosomal DNA restriction analysis (ARDRA) and grouped into 30 different genotypes. Whereas almost the same numbers of different genotypes were observed at both sampling times when considering all microenvironments, important changes in their evenness were observed. At the microscale level, we also noticed a heterogeneous distribution of the genotypes. Partial 16S rDNA sequences of each genotype were determined to permit phylogenetic affiliation. Whereas Pseudomonas-like species were dominant in all microenvironments at T = 0, genotypes not detected before spiking such as genotypes closely related to Xanthomonas, Pseudoaminobacter, and Sphingomonas-like species became dominant at T = 30. Similarly, several genotypes close to Bacillus, Streptomyces, and Rhodococcus species were only detected in the sand fractions at T = 0 and could not be detected in these fractions at T = 30. Probes defined within the intergenic spacer between the rrs and rrl genes were designed for the dominant genotypes and were hybridized toward the RISA (Ribosomal Intergenic Spacer Analysis) profiles derived from the T = 0 and T = 30 bacterial communities associated to the unfractionated soil. Results showed that the culturable dominant HgR genotypes partially contributed to the adaptation of the whole bacterial community.

Characterization of bacterial and fungal soil communities by automated ribosomal intergenic spacer analysis fingerprints: biological and methodological variability

Automated rRNA intergenic spacer analysis (ARISA) was used to characterise bacterial (B-ARISA) and fungal (F-ARISA) communities from different soil types. The 16S-23S intergenic spacer region from the bacterial rRNA operon was amplified from total soil community DNA for B-ARISA. Similarly, the two internal transcribed spacers and the 5.8S rRNA gene (ITS1-5.8S-ITS2) from the fungal rRNA operon were amplified from total soil community DNA for F-ARISA. Universal fluorescence-labeled primers were used for the PCRs, and fragments of between 200 and 1,200 bp were resolved on denaturing polyacrylamide gels by use of an automated sequencer with laser detection. Methodological (DNA extraction and PCR amplification) and biological (inter- and intrasite) variations were evaluated by comparing the number and intensity of peaks (bands) between electrophoregrams (profiles) and by multivariate analysis. Our results showed that ARISA is a high-resolution, highly reproducible technique and is a robust method for discriminating between microbial communities. To evaluate the potential biases in community description provided by ARISA, we also examined databases on length distribution of ribosomal intergenic spacers among bacteria (L. Ranjard, E. Brothier, and S. Nazaret, Appl. Environ. Microbiol. 66:5334-5339, 2000) and fungi.

Quantitative and qualitative microscale distribution of bacteria in soil

Soil structure represents a mosaic of microenvironments differing in their physical, chemical and biological properties. At a microscale level, such structural organisation consequently provides different habitats in which indigenous bacteria are heterogenously distributed. This review provides an overview of the methodologies useful to microbiologists for assessing spatial distribution of bacteria in soil, and quantitative and qualitative bacterial distribution for determining the preferential location of bacteria and the definition of "favourable" habitats.

Comparison of nifH gene pools in soils and soil microenvironments with contrasting properties

The similarities and differences in the structures of the nifH gene pools of six different soils (Montrond, LCSA-p, Vernon, Dombes, LCSA-c, and Thysse Kaymor) and five soil fractions extracted from LCSA-c were studied. Bacterial DNA was directly extracted from the soils, and a region of the nifH gene was amplified by PCR and analyzed by restriction. Soils were selected on the basis of differences in soil management, plant cover, and major physicochemical properties. Microenvironments differed on the basis of the sizes of the constituent particles and the organic carbon and clay contents. Restriction profiles were subjected to principal-component analysis. We showed that the composition of the diazotrophic communities varied both on a large scale (among soils) and on a microscale (among microenvironments in LCSA-c soil). Soil management seemed to be the major parameter influencing differences in the nifH gene pool structure among soils by controlling inorganic nitrogen content and its variation. However, physicochemical parameters (texture and total C and N contents) were found to correlate with differences among nifH gene pools on a microscale. We hypothesize that the observed nifH genetic structures resulted from the adaptation to fluctuating conditions (cultivated soil, forest soil, coarse fractions) or constant conditions (permanent pasture soil, fine fractions). We attempted to identify a specific band within the profile of the clay fraction by cloning and sequencing it and comparing it with the gene databases. Unexpectedly, the nifH sequences of the dominant bacteria were most similar to sequences of unidentified marine eubacteria.

Sequencing bands of ribosomal intergenic spacer analysis fingerprints for characterization and microscale distribution of soil bacterium populations responding to mercury spiking

Two major emerging bands (a 350-bp band and a 650-bp band) within the RISA (ribosomal intergenic spacer analysis) profile of a soil bacterial community spiked with Hg(II) were selected for further identification of the populations involved in the response of the community to the added metal. The bands were cut out from polyacrylamide gels, cloned, characterized by restriction analysis, and sequenced for phylogenetic affiliation of dominant clones. The sequences were the intergenic spacer between the rrs and rrl genes and the first 130 nucleotides of the rrl gene. Comparison of sequences derived from the 350-bp band to The GenBank database permitted us to identify the bacteria as being mostly close relatives to low G+C firmicutes (Clostridium-like genera), while the 650-bp band permitted us to identify the bacteria as being mostly close relatives to beta-proteobacteria (Ralstonia-like genera). Oligonucleotide probes specific for the identified dominant bacteria were designed and hybridized with the RISA profiles derived from the control and spiked communities. These studies confirmed the contribution of these populations to the community response to the metal. Hybridization of the RISA profiles from subcommunities (bacterial pools associated with different soil microenvironments) also permitted to characterize the distribution and the dynamics of these populations at a microscale level following mercury spiking.

Heterogeneous Cell Density and Genetic Structure of Bacterial Pools Associated with Various Soil Microenvironments as Determined by Enumeration and DNA Fingerprinting Approach (RISA)

The cell density and the genetic structure of bacterial subcommunities (further named pools) present in the various microenvironments of a silt loam soil were investigated. The microenvironments were isolated first using a procedure of soil washes that separated bacteria located outside aggregates (outer part) from those located inside aggregates (inner part). A nondestructive physical fractionation was then applied to the inner part in order to separate bacteria located inside stable aggregates of different size (size fractions, i.e., two macroaggregate fractions, two microaggregate fractions, and the dispersible day fraction). Bacterial densities measured by acridine orange direct counts (AODC) and viable heterotrophic (VH) cell enumerations showed the heterogeneous quantitative distribution of cells in soil. Bacteria were preferentially located in the inner part with 87.6% and 95.4% of the whole AODC and VH bacteria, respectively, and in the microaggregate and dispersible clay fractions of this part with more than 70% and 80% of the whole AODC and VH bacteria, respectively. The rRNA intergenic spacer analysis (RISA) was used to study the genetic structure of the bacterial pools. Different fingerprints and consequently different genetic structures were observed between the unfractionated soil and the microenvironments, and also among the various microenvironments, giving evidence that some populations were specific to a given location in addition to the common populations of all the microenvironments. Cluster and multivariate analysis of RISA profiles showed the weak contribution of the pools located in the macroaggregate fractions to the whole soil community structure, as well as the clear distinction between the pool associated to the macroaggregate fractions and the pools associated to the microaggregate ones. Furthermore, these statistical analyses allowed us to ascertain the influence of the clay and organic matter content of microenvironments on the genetic structure relatedness between pools.

Monitoring complex bacterial communities using culture-independent molecular techniques: application to soil environment

Over the last decade, important advances in molecular biology led to the development of culture-independent approaches to describing bacterial communities. These new strategies, based on the analysis of DNA directly extracted from environmental samples, circumvent the steps of isolation and culturing of bacteria, which are known for their selectivity leading to a non-representative view of the extent of bacterial diversity. This review provides an overview of the potentials and limitations of some molecular approaches currently used in microbial ecology. Examples of applications to the study of indigenous soil microbial community illustrate the feasibility and the power of such approaches.

A soil microscale study to reveal the heterogeneity of Hg(II) impact on indigenous bacteria by quantification of adapted phenotypes and analysis of community DNA fingerprints

The short term impact of 50 µM Hg(II) on soil bacterial community structure was evaluated in different microenvironments of a silt loam soil in order to determine the contribution of bacteria located in these microenvironments to the overall bacterial response to mercury spiking. Microenvironments and associated bacteria, designated as bacterial pools, were obtained by successive soil washes to separate the outer fraction, containing loosely associated bacteria, and the inner fraction, containing bacteria retained into aggregates, followed by a physical fractionation of the inner fraction to separate aggregates according to their size (size fractions). Indirect enumerations of viable heterotrophic (VH) and resistant (Hg(R)) bacteria were performed before and 30 days after mercury spiking. A ribosomal intergenic spacer analysis (RISA), combined with multivariate analysis, was used to compare modifications at the community level in the unfractionated soil and in the microenvironments. The spatial heterogeneity of the mercury impact was revealed by a higher increase of Hg(R) numbers in the outer fraction and in the coarse size fractions. Furthermore, shifts in RISA patterns of total community DNA indicated changes in the composition of the dominant bacterial populations in response to Hg(II) stress in the outer and in the clay size fractions. The heterogeneity of metal impact on indigenous bacteria, observed at a microscale level, is related to both the physical and chemical characteristics of the soil microenvironments governing mercury bioavailability and to the bacterial composition present before spiking.