Impact of Cultivation Substrate and Microbial Community on Improving Mushroom Productivity: A Review

Simple Summary

Lignocellulosic material and substrate formulations affect mushroom productivity. The microbial community in cultivation substrates affects the quality of the substrates and the efficiency of mushroom production. The elucidation of the key microbes and their biochemical function can serve as a useful guide in the development of a more effective system for mushroom cultivation.

Abstract

Lignocellulosic materials commonly serve as base substrates for mushroom production. Cellulose, hemicellulose, and lignin are the major components of lignocellulose materials. The composition of these components depends upon the plant species. Currently, composted and non-composted lignocellulosic materials are used as substrates in mushroom cultivation depending on the mushroom species. Different substrate compositions can directly affect the quality and quantity of mushroom production yields. Consequently, the microbial dynamics and communities of the composting substrates can significantly affect mushroom production. Therefore, changes in both substrate composition and microbial diversity during the cultivation process can impact the production of high-quality substrates and result in a high degree of biological efficiency. A brief review of the current findings on substrate composition and microbial diversity for mushroom cultivation is provided in this paper. We also summarize the advantages and disadvantages of various methods of mushroom cultivation by analyzing the microbial diversity of the composting substrates during mushroom cultivation. The resulting information will serve as a useful guide for future researchers in their attempts to increase mushroom productivity through the selection of suitable substrate compositions and their relation to the microbial community.

Plant growth promoting rhizobacterial diversity in potato grown soil in the Gwalior region of India

There seems to be meager studies with regards to rhizo and non-rhizo microbial association with potato plant from the central India. Present study was undertaken to evaluate the microbial diversity of rhizospheric and non-rhizospheric isolates from three varieties of potato viz Kufri sindhuri, Kufri lauvkar and Kufri chipsona-3 procured from the Central Potato Research Station, Maharajpura, Gwalior. A total of 130 bacterial forms were isolated, and amongst these forty isolates were further characterized on their morphological basis, and those showing some of PGPR characteristics were identified to species level using VITEK-2 method. Various bacterial populations were found in potato rhizosphere and dominant presence was those of Bacillus subtilis, Bacillus Megaterium and Lysinibacillus sphaericus. The non-rhizospheric soil was dominant in the forms like Aeromonas salmonicida, Morxella group and Bacillus coagulans. Highest bacterial diversity was found in the rhizosphere soil of different potato cultivars than in the non-rhizospheric soil of potato.

Oral mycobiome identification in atopic dermatitis, leukemia, and HIV patients - a systematic review

INTRODUCTION

Oral mycobiome profiling is important to understand host-pathogen interactions that occur in various diseases. Invasive fungal infections are particularly relevant for patients who have received chemotherapy and for those who have HIV infection. In addition, changes in fungal microbiota are associated with the worsening of chronic conditions like atopic dermatitis (AD). This work aims, through a systematic review, to analyze the methods used in previous studies to identify oral fungi and their most frequent species in patients with the following conditions: HIV infection, leukemia, and atopic dermatitis.

METHODS

A literature search was performed on several different databases. Inclusion criteria were: written in English or Portuguese; published between September 2009 and September 2019; analyzed oral fungi of HIV-infected, leukemia, or AD patients.

RESULTS

21 studies were included and the most identified species was Candida. The predominant methods of identification were morphological (13/21) and sugar fermentation and assimilation tests (11/21). Polymerase chain reaction (PCR) was the most used molecular method (8/21) followed by sequencing techniques (3/21).

CONCLUSIONS

Although morphological and biochemical tests are still used, they are associated with high-throughput sequencing techniques, due to their accuracy and time saving for profiling the predominant species in oral mycobiome.

Horizontal transfer and finalization of a reliable detection method for the olive fruit fly endosymbiont, Candidatus Erwinia dacicola

BACKGROUND

The olive fly, Bactrocera oleae, is the most important insect pest in olive production, causing economic damage to olive crops worldwide. In addition to extensive research on B. oleae control methods, scientists have devoted much effort in the last century to understanding olive fly endosymbiosis with a bacterium eventually identified as Candidatus Erwinia dacicola. This bacterium plays a relevant role in olive fly fitness. It is vertically transmitted, and it benefits both larvae and adults in wild populations; however, the endosymbiont is not present in lab colonies, probably due to the antibiotics and preservatives required for the preparation of artificial diets. Endosymbiont transfer from wild B. oleae populations to laboratory-reared ones allows olive fly mass-rearing, thus producing more competitive flies for future Sterile Insect Technique (SIT) applications.

RESULTS

We tested the hypothesis that Ca. E. dacicola might be transmitted from wild, naturally symbiotic adults to laboratory-reared flies. Several trials have been performed with different contamination sources of Ca. E. dacicola, such as ripe olives and gelled water contaminated by wild flies, wax domes containing eggs laid by wild females, cages dirtied by faeces dropped by wild flies and matings between lab and wild adults. PCR-DGGE, performed with the primer set 63F-GC/518R, demonstrated that the transfer of the endosymbiont from wild flies to lab-reared ones occurred only in the case of cohabitation.

CONCLUSIONS

Cohabitation of symbiotic wild flies and non-symbiotic lab flies allows the transfer of Ca. E. dacicola through adults. Moreover, PCR-DGGE performed with the primer set 63F-GC/518R was shown to be a consistent method for screening Ca. E. dacicola, also showing the potential to distinguish between the two haplotypes (htA and htB). This study represents the first successful attempt at horizontal transfer of Ca. E. dacicola and the first step in acquiring a better understanding of the endosymbiont physiology and its relationship with the olive fly. Our research also represents a starting point for the development of a laboratory symbiotic olive fly colony, improving perspectives for future applications of the Sterile Insect Technique.

Exploring the diversity and dynamic of bacterial community vertically distributed in Tongguling National Nature Reserve in Hainan Island, China

National nature reserves are important for preserving ecological resources and constructing national ecological security barriers. Tongguling National Nature Reserve (TNNR) is known for its unique tropical island ecosystem and abundant biological resources. This study was conducted to characterize and compare its bacterial community diversity and composition in soils from 10, 20, and 30 cm in depth using high-throughput sequencing of 16S rDNA genes. We found that soils from 20 cm had the highest diversity and might serve as a "middle bridge" to the dynamic distribution between the 10- and 30-cm soil samples. The diversity pattern indicated that the main abundant groups varied distinctly and significantly among soils of different depths. Moreover, Chloroflexi was the most dynamic group in TNNR soils, together with another abundant but rarely reported group, Verrucomicrobia, which greatly enhanced the microbial diversity of TNNR soils. Overall, the results of this study emphasize the urgent need for greater understanding of bacterial community variations in response to human activities and climate change.

Evaluating the impact of the biocontrol agent Trichoderma harzianum ITEM 3636 on indigenous microbial communities from field soils

AIM

To investigate the impact of inoculating peanut seeds with the biocontrol agent Trichoderma harzianum ITEM 3636 on the structure of bacterial and fungal communities from agricultural soils.

METHODS AND RESULTS

Polymerase chain reaction (PCR)-denaturing gradient gel electrophoresis (PCR-DGGE) and next-generation sequencing (NGS) of amplicons (or marker gene amplification metagenomics) were performed to investigate potential changes in the structure of microbial communities from fields located in a peanut-producing area in the province of Córdoba, Argentina. Fields had history of peanut smut (caused by Thecaphora frezii) incidence. The Shannon indexes (H'), which estimate diversity, obtained from the PCR-DGGE assays did not show significant differences neither for bacterial nor for fungal communities between control and inoculation treatments. On the other hand, the number of operational taxonomic units obtained after NGS was similar between all the analysed samples. Moreover, results of alpha and beta diversity showed that there were no significant variations between the relative abundances of the most representative bacterial and fungal phyla and genera, in both fields.

CONCLUSIONS

Trichoderma harzianum ITEM 3636 decreases the incidence and severity of agriculturally relevant diseases without causing significant changes in the microbial communities of agricultural soils.

SIGNIFICANCE AND IMPACT OF THE STUDY

Our investigations provide information on the structure of bacterial and fungal communities in peanut-producing fields after inoculation of seeds with a biocontrol agent.

16S rRNA analysis of diversity of manure microbial community in dairy farm environment

Dairy farms generate a considerable amount of manure, which is applied in cropland as fertilizer. While the use of manure as fertilizer reduces the application of chemical fertilizers, the main concern with regards to manure application is microbial pollution. Manure is a reservoir of a broad range of microbial populations, including pathogens, which have potential to cause contamination and pose risks to public and animal health. Despite the widespread use of manure fertilizer, the change in microbial diversity of manure under various treatment processes is still not well-understood. We hypothesize that the microbial population of animal waste changes with manure handling used in a farm environment. Consequential microbial risk caused by animal manure may depend on manure handling. In this study, a reconnaissance effort for sampling dairy manure in California Central Valley followed by 16S rRNA analysis of content and diversity was undertaken to understand the microbiome of manure after various handling processes. The microbial community analysis of manure revealed that the population in liquid manure differs from that in solid manure. For instance, the bacteria of genus Sulfuriomonas were unique in liquid samples, while the bacteria of genus Thermos were observed only in solid samples. Bacteria of genus Clostridium were present in both solid and liquid samples. The population among liquid samples was comparable, as was the population among solid samples. These findings suggest that the mode of manure application (i.e., liquid versus solid) could have a potential impact on the microbiome of cropland receiving manure as fertilizers.

Temporal dynamic of parasite-mediated linkages between the forest canopy and soil processes and the microbial community

Parasitic plants are important drivers of community and ecosystem properties. In this study, we identify different mechanisms by which mistletoe (Viscum album subsp. austriacum) can affect soil chemical and biological properties at different temporal stages of parasitism. We quantified the effect of parasitism on host growth and the number of frugivorous mutualists visiting the host canopy. Then we collected, identified, and weighed the organic matter input underneath tree canopies and analyzed its nutrient content. Simultaneously, we analyzed soil samples under tree canopies and examined the chemical properties, microbial abundance, and functional evenness of heterotrophic microbial communities. Mistletoe increased the amount, quality, and diversity of organic matter input beneath the host canopy, directly through its nutrient-rich litter and indirectly through a reduction in host litterfall and an increase in bird-derived debris. All these effects gave rise to enriched hotspots able to support larger and more functionally even soil microbial communities beneath parasitized hosts, the effects of which were accentuated after host death. We conclude that mistletoe, together with the biotic interactions it mediates, plays a key role in intensifying soil resource availability, regulating the functional evenness, abundance, and spatial distribution of soil microbial communities.

Response of N₂O emissions to elevated water depth regulation: comparison of rhizosphere versus non-rhizosphere of Phragmites australis in a field-scale study

Emissions of nitrous oxide (N2O) from wetland ecosystems are globally significant and have recently received increased attention. However, relatively few direct studies of these emissions in response to water depth-related changes in sediment ecosystems have been conducted, despite the likely role they play as hotspots of N2O production. We investigated depth-related differential responses of the dissolved inorganic nitrogen distribution in Phragmites australis (Cav.) Trin. ex Steud. rhizosphere versus non-rhizosphere sediments to determine if they accelerated N2O emissions and the release of inorganic nitrogen. Changes in static water depth and P. australis growth both had the potential to disrupt the distribution of porewater dissolved NH4 (+), NO3 (-), and NO2 (-) in profiles, and NO3 (-) had strong surface aggregation tendency and decreased significantly with depth. Conversely, the highest NO2 (-) contents were observed in deep water and the lowest in shallow water in the P. australis rhizosphere. When compared with NO3 (-), NH4 (+), and NO2 (-), fluxes from the rhizosphere were more sensitive to the effects of water depth, and both fluxes increased significantly at a depth of more than 1 m. Similarly, N2O emissions were obviously accelerated with increasing depth, although those from the rhizosphere were more readily controlled by P. australis. Pearson's correlation analysis showed that water depth was significantly related to N2O emission and NO2 (-) fluxes, and N2O emissions were also strongly dependent on NO2 (-) fluxes (r = 0.491, p < 0.05). The results presented herein provide new insights into inorganic nitrogen biogeochemical cycles in freshwater sediment ecosystems.

Modern molecular approaches for analyzing microbial diversity from mushroom compost ecosystem

Biosphere is a store house of various microorganisms that may be employed to isolate and exploit microbes for environmental, pharmaceutical, agricultural and industrial applications. There is restricted data regarding the structure and dynamics of microbial communities in several ecosystems because only a little fraction of microbial diversity is accessible by culture methods. Owing to limitations of traditional enrichment methods and pure culture techniques, microbiological studies have offered a narrow portal for investigating microbial flora. The bacterial community represented by the morphological and nutritional criteria failed to provide a natural taxonomic order according to the evolutionary relationship. Genetic diversity among the isolates recovered from mushroom compost has not been widely studied. To understand genetic diversity and community composition of the mushroom compost microflora, different approaches are now followed by taxonomists, to characterize and identify isolates up to species level. Molecular microbial ecology is an emerging discipline of biology under molecular approach which can provide complex community profiles along with useful phylogenetic information. The genomic era has resulted in the development of new molecular tools and techniques for study of culturable microbial diversity including the DNA base ratio (mole% G + C), DNA-DNA hybridization, DNA microarray and reverse sample genome probing. In addition, non-culturable diversity of mushroom compost ecosystem can be characterized by employing various molecular tools which would be discussed in the present review.

Diversity and phylogenetic analysis of endosymbiotic bacteria of the date palm root borer Oryctes agamemnon (Coleoptera: Scarabaeidae)

BACKGROUND

The date palm root borer Oryctes agamemnon (Coleoptera: Scarabaeidae) is one of the major pests of palms. In Saudi Arabia, both larvae and adults of Oryctes are particularly troublesome, especially during the establishment of young date palm orchards. Endosymbiotic bacteria are known to have a key role in food digestion and insecticide resistance mechanisms, and therefore are essential to their host insect. Identification of these bacteria in their insect host can lead to development of new insect pest control strategies.

RESULTS

Metagenomic DNA from larval midgut of the date palm root borer, O. agamemnon, was analyzed for endosymbiotic bacterial communities using denatured gradient gel electrophoresis (DGGE) utilizing 16S rRNA genes. The DGGE fingerprints with metagenomic DNA showed predominance of eleven major operational taxonomic units (OTUs) identified as members of Photobacterium, Vibrio, Allomonas, Shewanella, Cellulomonas, and Citrobacter, as well as uncultured bacteria, including some uncultured Vibrio members. DGGE profiles also showed shifts in the dominant bacterial populations of the original soil compared with those that existed in the larval midguts. The endosymbiotic bacterial community was dominated by members of the family Vibrionaceae (54.5%), followed by uncultured bacteria (18.2%), Enterobacteriaceae (9.1%), Shewanellaceae (9.1%), and Cellulomonadaceae (9.1%). Phylogenetic studies confirmed the affiliation of the dominant OTUs into specified families revealed by clustering of each phylotype to its corresponding clade. Relative frequency of each phylotype in larval midguts revealed predominance of Vibrio furnisii and Vibrio navarrensis, followed by uncultured bacterial spp., then Cellulomonas hominis, Shewanella algae, and Citrobacter freundii.

CONCLUSION

Analysis of metagenomic DNA for endosymbiotic bacterial communities from the midgut of Oryctes larvae showed strong selection of specific bacterial populations that may have a key role in digestion, as well as other benefits to the larvae of O. agamemnon. Determination of the distinct endosymbiotic community structure and its possible biological functions within the insect could provide us with basic information for future pest control research.

Quantification and characterization of microbial biofilm community attached on the surface of fermentation vessels used in green table olive processing

The aim of the present study was the quantification of biofilm formed on the surface of plastic vessels used in Spanish-style green olive fermentation and the characterization of the biofilm community by means of molecular fingerprinting. Fermentation vessels previously used in green olive processing were subjected to sampling at three different locations, two on the side and one on the bottom of the vessel. Prior to sampling, two cleaning treatments were applied to the containers, including (a) washing with hot tap water (60 °C) and household detergent (treatment A) and (b) washing with hot tap water, household detergent and bleach (treatment B). Population (expressed as log CFU/cm(2)) of total viable counts (TVC), lactic acid bacteria (LAB) and yeasts were enumerated by standard plating. Bulk cells (whole colonies) from agar plates were isolated for further characterization by PCR-DGGE. Results showed that regardless of the cleaning treatment no significant differences were observed between the different sampling locations in the vessel. The initial microbial population before cleaning ranged between 3.0-4.5 log CFU/cm(2) for LAB and 4.0-4.6 log CFU/cm(2) for yeasts. Cleaning treatments exhibited the highest effect on LAB that were recovered at 1.5 log CFU/cm(2) after treatment A and 0.2 log CFU/cm(2) after treatment B, whereas yeasts were recovered at approximately 1.9 log CFU/cm(2) even after treatment B. High diversity of yeasts was observed between the different treatments and sampling spots. The most abundant species recovered belonged to Candida genus, while Wickerhamomyces anomalus, Debaryomyces hansenii and Pichia guilliermondii were frequently detected. Among LAB, Lactobacillus pentosus was the most abundant species present on the abiotic surface of the vessels.

Bacteria abundance and diversity of different life stages of Plutella xylostella (Lepidoptera: Plutellidae), revealed by bacteria culture-dependent and PCR-DGGE methods

Microbial abundance and diversity of different life stages (fourth instar larvae, pupae and adults) of the diamondback moth, Plutella xylostella L., collected from field and reared in laboratory, were investigated using bacteria culture-dependent method and PCR-DGGE analysis based on the sequence of bacteria 16S rRNA V3 region gene. A large quantity of bacteria was found in all life stages of P. xylostella. Field population had higher quantity of bacteria than laboratory population, and larval gut had higher quantity than pupae and adults. Culturable bacteria differed in different life stages of P. xylostella. Twenty-five different bacterial strains were identified in total, among them 20 strains were presented in larval gut, only 8 strains in pupae and 14 strains in adults were detected. Firmicutes bacteria, Bacillus sp., were the most dominant species in every life stage. 15 distinct bands were obtained from DGGE electrophoresis gel. The sequences blasted in GenBank database showed these bacteria belonged to six different genera. Phylogenetic analysis showed the sequences of the bacteria belonged to the Actinobacteri, Proteobacteria and Firmicutes. Serratia sp. in Proteobacteria was the most abundant species in larval gut. In pupae, unculturable bacteria were the most dominant species, and unculturable bacteria and Serratia sp. were the most dominant species in adults. Our study suggested that a combination of molecular and traditional culturing methods can be effectively used to analyze and to determine the diversity of gut microflora. These known bacteria may play important roles in development of P. xylostella.

Bioinformatic progress and applications in metaproteogenomics for bridging the gap between genomic sequences and metabolic functions in microbial communities

Metaproteomics of microbial communities promises to add functional information to the blueprint of genes derived from metagenomics. Right from its beginning, the achievements and developments in metaproteomics were closely interlinked with metagenomics. In addition, the evaluation, visualization, and interpretation of metaproteome data demanded for the developments in bioinformatics. This review will give an overview about recent strategies to use genomic data either from public databases or organismal specific genomes/metagenomes to increase the number of identified proteins obtained by mass spectrometric measurements. We will review different published metaproteogenomic approaches in respect to the used MS pipeline and to the used protein identification workflow. Furthermore, different approaches of data visualization and strategies for phylogenetic interpretation of metaproteome data are discussed as well as approaches for functional mapping of the results to the investigated biological systems. This information will in the end allow a comprehensive analysis of interactions and interdependencies within microbial communities.

Relationship between communities and processes; new insights from a field study of a contaminated ecosystem

We used a 93-year-old mine waste contamination gradient in alluvial soil to explore the relationship between ecosystem level functioning and community structure in a chronically stressed ecosystem. The sensitivity of broad functional parameters (in situ soil respiration, microbial biomass, above and below ground plant biomass) and microbial diversity [phospholipid fatty acid (PLFA) abundance and richness] were compared. Functional responses were linear with respect to contaminants while thresholds were detected in the community structural response to contamination along the gradient. For example, in situ soil respiration was negatively and linearly correlated to contamination concentration (R = -0.783, P < 0.01), but changes in microbial community structure only became evident where contaminant concentrations were greater than 28 times above background levels. Our results suggest that functional redundancy does not prevent depression of ecosystem function in the long-term.

Quantifying species diversity with a DNA barcoding-based method: Tibetan moth species (Noctuidae) on the Qinghai-Tibetan Plateau

With the ongoing loss of biodiversity, there is a great need for fast and effective ways to assess species richness and diversity: DNA barcoding provides a powerful new tool for this. We investigated this approach by focusing on the Tibetan plateau, which is one of the world's top biodiversity hotspots. There have been few studies of its invertebrates, although they constitute the vast majority of the region's diversity. Here we investigated species diversity of the lepidopteran family Noctuidae, across different environmental gradients, using measurements based on traditional morphology as well as on DNA barcoding. The COI barcode showed an average interspecific K2P distance of 9.45±2.08%, which is about four times larger than the mean intraspecific distance (1.85±3.20%). Using six diversity indices, we did not detect any significant differences in estimated species diversity between measurements based on traditional morphology and on DNA barcoding. Furthermore, we found strong positive correlations between them, indicating that barcode-based measures of species diversity can serve as a good surrogate for morphology-based measures in most situations tested. Eastern communities were found to have significantly higher diversity than Western ones. Among 22 environmental factors tested, we found that three (precipitation of driest month, precipitation of driest quarter, and precipitation of coldest quarter) were significantly correlated with species diversity. Our results indicate that these factors could be the key ecological factors influencing the species diversity of the lepidopteran family Noctuidae on the Tibetan plateau.

Protein-based stable isotope probing (protein-SIP) in functional metaproteomics

The community phenotype as the sum of molecular functions of organisms living in consortia strongly depends on interactions within these communities. Therefore, the analyses of the most significant molecules in terms of the phenotype, the proteins, have to be performed on samples without disrupting the meta-species environment. Due to the increasing genomic information, proteins provide insights into a potential molecular function and the phylogenetic structure of the community. Unfortunately, the lists of identified proteins are often based first on the technical capacity of the used methods or instruments, and second on the interpretation of them by the assignment of molecular functions to proteins in databases. Especially in non-model organisms the functions of many proteins are often not known and an increasing number of studies indicate a significant amount of uncertainty. To decrease the dependency on assumptions and to enable functional insights by metaproteome approaches, the metabolic labeling from an isotopically labeled substrate can be used. Since the metabolites deriving from the substrate are very rarely species-specific, the incorporation of the stable isotope into proteins can be used as a surrogate marker for metabolic activity. The degree of incorporation can be determined accurately on the peptide level by mass spectrometry; additionally, the peptide sequence provides information on the metabolic active species. Thereby, protein-stable isotope probing (protein-SIP) adds functional information to metaproteome approaches. The classical metaproteome approaches will be reviewed with an emphasis on their attempts towards functional interpretation. The gain from functional insights into metaproteomics by using metabolic labeling of stable isotopes of carbon, nitrogen, and sulfur is reviewed with a focus on the techniques of measurement, calculation of incorporation and data processing.

The gut bacteria associated with Camponotus japonicus Mayr with culture-dependent and DGGE methods

The bacterial composition and distribution in the different gut regions of Camponotus japonicus were investigated using both culture-dependent method and culture-independent method of polymerase chain reaction and denaturing gradient gel electrophoresis (PCR-DGGE). Five different bacterial strains were isolated using culture-dependent method, and they all belong to the phylum Firmicutes, including three genera of bacteria Bacillus, Paenibacillus, and Enterococcus. Bacillus cereus and Enterococcus mundtii were found in the midgut; Paenibacillus sp. was isolated from the hindgut; and the other two Bacillus spp. were isolated from the crop. Twelve distinct DGGE bands were found using PCR-DGGE method, and their sequences blasting analysis shows that they are members of the Proteobacteria and the Firmicutes, respectively, including three genera (Pseudomonas, Candidatus Blochmannia, Fructobacillus) and one uncultured bacterium, in which Pseudomonas was the most dominant bacteria group in all the three gut regions. According to the DGGE profile, the three gut regions had very similar gut communities, and all the DGGE bands were presented in the midgut and hindgut, while just two bands representing Blochmannia were not present in the crop. The results of our study indicate that the gut of C. japonicus harbors several other bacteria besides the obligate endosymbionts Blochmannia, and more work should be carried on to verify if they are common in the guts of other Camponotus ants.

A cost-effective and universal strategy for complete prokaryotic genomic sequencing proposed by computer simulation

BACKGROUND

Pyrosequencing techniques allow scientists to perform prokaryotic genome sequencing to achieve the draft genomic sequences within a few days. However, the assemblies with shotgun sequencing are usually composed of hundreds of contigs. A further multiplex PCR procedure is needed to fill all the gaps and link contigs into complete chromosomal sequence, which is the basis for prokaryotic comparative genomic studies. In this article, we study various pyrosequencing strategies by simulated assembling from 100 prokaryotic genomes.

FINDINGS

Simulation study shows that a single end 454 Jr. run combined with a paired end 454 Jr. run (8 kb library) can produce: 1) ~90% of 100 assemblies with < 10 scaffolds and ~95% of 100 assemblies with < 150 contigs; 2) average contig N50 size is over 331 kb; 3) average single base accuracy is > 99.99%; 4) average false gene duplication rate is < 0.7%; 5) average false gene loss rate is < 0.4%.

CONCLUSIONS

A single end 454 Jr. run combined with a paired end 454 Jr. run (8 kb library) is a cost-effective way for prokaryotic whole genome sequencing. This strategy provides solution to produce high quality draft assemblies for most of prokaryotic organisms within days. Due to the small number of assembled scaffolds, the following multiplex PCR procedure (for gap filling) would be easy. As a result, large scale prokaryotic whole genome sequencing projects may be finished within weeks.

Structure and diversity of bacterial, eukaryotic and archaeal communities in glacial cryoconite holes from the Arctic and the Antarctic

The cryosphere presents some of the most challenging conditions for life on earth. Nevertheless, (micro)biota survive in a range of niches in glacial systems, including water-filled depressions on glacial surfaces termed cryoconite holes (centimetre to metre in diameter and up to 0.5 m deep) that contain dark granular material (cryoconite). In this study, the structure of bacterial and eukaryotic cryoconite communities from ten different locations in the Arctic and Antarctica was compared using T-RFLP analysis of rRNA genes. Community structure varied with geography, with greatest differences seen between communities from the Arctic and the Antarctic. DNA sequencing of rRNA genes revealed considerable diversity, with individual cryoconite hole communities containing between six and eight bacterial phyla and five and eight eukaryotic 'first-rank' taxa and including both bacterial and eukaryotic photoautotrophs. Bacterial Firmicutes and Deltaproteobacteria and Epsilonproteobacteria, eukaryotic Rhizaria, Haptophyta, Choanomonada and Centroheliozoa, and archaea were identified for the first time in cryoconite ecosystems. Archaea were only found within Antarctic locations, with the majority of sequences (77%) related to members of the Thaumarchaeota. In conclusion, this research has revealed that Antarctic and Arctic cryoconite holes harbour geographically distinct highly diverse communities and has identified hitherto unknown bacterial, eukaryotic and archaeal taxa, therein.

Temporal variation of β-diversity and assembly mechanisms in a bacterial metacommunity

The turnover of community composition across space, β-diversity, is influenced by different assembly mechanisms, which place varying weight on local habitat factors, such as environmental conditions and species interactions, and regional factors such as dispersal and history. Several assembly mechanisms may function simultaneously; however, little is known about how their importance changes over time and why. Here, we implemented a field survey where we sampled a bacterial metacommunity consisting of 17 rock pools located at the Swedish Baltic Sea coast at 11 occasions during 1 year. We determined to which extent communities were structured by different assembly mechanisms using variation partitioning and studied changes in β-diversity across environmental gradients over time. β-Diversity was highest at times of high overall productivity and environmental heterogeneity in the metacommunity, at least partly due to species sorting, that is, selection of taxa by the prevailing environmental conditions. In contrast, dispersal-driven assembly mechanisms were primarily detected at times when β-diversity was relatively low. There were no indications for strong and persistent differences in community composition or β-diversity between permanent and temporary pools, indicating that the physical disturbance regime is of relatively minor importance. In summary, our study clearly suggests that there are temporal differences in the relative importance of different assembly mechanisms related to abiotic factors and shows that the temporal variability of those factors is important for a more complete understanding of bacterial metacommunity dynamics.

Epigeic earthworms exert a bottleneck effect on microbial communities through gut associated processes

Background

Earthworms play a critical role in organic matter decomposition because of the interactions they establish with microorganisms. The ingestion, digestion, assimilation of organic material in the gut and then casting is the first step in earthworm-microorganism interactions. The current knowledge of these direct effects is still limited for epigeic earthworm species, mainly those living in man-made environments. Here we tested whether and to what extent the earthworm Eisenia andrei is capable of altering the microbiological properties of fresh organic matter through gut associated processes; and if these direct effects are related to the earthworm diet.

Methodology

To address these questions we determined the microbial community structure (phospholipid fatty acid profiles) and microbial activity (fluorescein diacetate hydrolysis) in the earthworm casts derived from three types of animal manure (cow, horse and pig manure), which differed in microbial composition.

Principal Findings

The passage of the organic material through the gut of E. andrei reduced the total microbial biomass irrespective of the type of manure, and resulted in a decrease in bacterial biomass in all the manures; whilst leaving the fungi unaffected in the egested materials. However, unlike the microbial biomass, no such reduction was detected in the total microbial activity of cast samples derived from the pig manure. Moreover, no differences were found between cast samples derived from the different types of manure with regards to microbial community structure, which provides strong evidence for a bottleneck effect of worm digestion on microbial populations of the original material consumed.

Conclusions/Significance

Our data reveal that earthworm gut is a major shaper of microbial communities, thereby favouring the existence of a reduced but more active microbial population in the egested materials, which is of great importance to understand how biotic interactions within the decomposer food web influence on nutrient cycling.

Detecting unknown sequences with DNA microarrays: explorative probe design strategies

Designing environmental DNA microarrays that can be used to survey the extreme diversity of microorganisms existing in nature, represents a stimulating challenge in the field of molecular ecology. Indeed, recent efforts in metagenomics have produced a substantial amount of sequence information from various ecosystems, and will continue to accumulate large amounts of sequence data given the qualitative and quantitative improvements in the next-generation sequencing methods. It is now possible to take advantage of these data to develop comprehensive microarrays by using explorative probe design strategies. Such strategies anticipate genetic variations and thus are able to detect known and unknown sequences in environmental samples. In this review, we provide a detailed overview of the probe design strategies currently available to construct both phylogenetic and functional DNA microarrays, with emphasis on those permitting the selection of such explorative probes. Furthermore, exploration of complex environments requires particular attention on probe sensitivity and specificity criteria. Finally, these innovative probe design approaches require exploiting newly available high-density microarray formats.

Euxinic freshwater hypolimnia promote bacterial endemicity in continental areas

Bacteria and archaea represent the vast majority of biodiversity on Earth. The ways that dynamic ecological and evolutionary processes interact in the microbial world are, however, poorly known. Here, we have explored community patterns of planktonic freshwater bacteria inhabiting stratified lakes with oxic/anoxic interfaces and euxinic (anoxic and sulfurous) water masses. The interface separates a well-oxygenated upper water mass (epilimnion) from a lower anoxic water compartment (hypolimnion). We assessed whether or not the vertical zonation of lakes promoted endemism in deeper layers by analyzing bacterial 16S rRNA gene sequences from the water column of worldwide distributed stratified lakes and applying a community ecology approach. Community similarity based on the phylogenetic relatedness showed that bacterial assemblages from the same water layer were more similar across lakes than to communities from different layer within lakes and that anoxic hypolimnia presented greater β-diversity than oxic epilimnia. Higher β-diversity values are attributable to low dispersal and small connectivity between community patches. In addition, surface waters had significant spatial but non-significant environmental components controlling phylogenetic β-diversity patterns, respectively. Conversely, the bottom layers were significantly correlated with environment but not with geographic distance. Thus, we observed different ecological mechanisms simultaneously acting on the same water body. Overall, bacterial endemicity is probably more common than previously thought, particularly in isolated and environmentally heterogeneous freshwater habitats. We argue for a microbial diversity conservation perspective still lacking in the global and local biodiversity preservation policies.

A new combination of extraction and derivatization methods that reduces the complexity and preparation time in determining phospholipid fatty acids in solid environmental samples

Combinations of three extraction methods (modified Folch method, modified Bligh and Dyer and microwave-assisted extraction (MAE)) and two derivatization methods (alkaline methanolysis and derivatization with trimethylsulfonium hydroxide (TMSH)) are compared for determining phospholipid fatty acids (PLFAs) in soil and solid organic samples (animal manures, compost and vermicompost). The modified Folch method rendered the greatest total amount of PLFAs and the highest yields of individual PLFA biomarkers; the effect was most apparent in the vermicompost samples. MAE rendered similar extraction yields as the modified Bligh and Dyer method (the most commonly used extraction method), although MAE is much simpler and faster. The highest conversion yields of PLFAs into fatty acid methyl esters were achieved with TMSH as the derivatization agent. The modified Folch method together with derivatization with TMSH was the least complex and time consuming method of determining microbial community structure in solid environmental samples.

New insight into biodegradation of polylactide (PLA)/clay nanocomposites using molecular ecological techniques

Novel molecular ecological techniques were used to study changes in microbial community structure and population during degradation of polylactide (PLA)/organically modified layered silicates (OMLS) nanocomposites. Cloned gene sequences belonging to members of the phyla Actinobacteria and Ascomycota comprized the most dominant groups of microorganisms during biodegradation of PLA/OMLS nanocomposites. Due to their numerical abundance, members of these microbial groups are likely to play an important role during biodegradation process. This paper presents new insights into the biodegradability of PLA/OMLS nanocomposites and highlights the importance of using novel molecular ecological techniques for in situ identification of new microorganisms involved in biodegradation of polymeric materials.

Novel two-dimensional DNA gel electrophoresis mapping for characterizing complex bacterial communities in environmental samples

Genomic DNA profiles such as denaturing gradient gel electrophoresis (DGGE), temporal temperature gradient gel electrophoresis (TTGE), and single-strand conformation polymorphism (SSCP) have been commonly used to characterize bacterial communities in environmental samples. We recently developed a two-dimensional gel electrophoresis (2-DGE) method with a combination of chain-length polymorphism analysis (CLPA) and DGGE analysis, in order to improve the DNA resolution and resolve complex environmental DNA fragments produced by polymerase chain reaction (PCR) amplification. The 2-DGE method can generate high-resolution DNA separation maps on the basis of the lengths and composition polymorphisms of DNA sequences. It can thus facilitate detailed analyses between bacterial communities in complex environmental systems such as soil or water. For the present paper, we further developed two novel 2-DGE methods using a combination of CLPA and TTGE (or CLPA and SSCP) and here describe their potential application to the characterization of bacterial communities in nature using clustering analyses. The results show that DNA amplicons can undergo more detailed separation by the two new mapping than by their corresponding 1-DGE fingerprints. Our findings also suggest that these two new 2-DGE mapping techniques are more easily carried out than previously described DGGE-based 2-DGE mapping because they do not require a chemical denaturing gradient gel.

Two-dimensional DNA gel electrophoresis mapping: a novel approach to diversity analysis of bacterial communities in environmental soil

The diversity analysis of bacteria is useful for the environmental assessment of soil. Traditional molecular-based methods such as denaturing gradient gel electrophoresis (DGGE) and terminal restriction fragment length polymorphism (T-RFLP) analysis achieve a low-resolution display of bacterial DNA fragments on a gel. To improve the resolution, a novel two-dimensional DNA gel electrophoresis (2-DGE) method was designed. This method can generate a high-resolution DNA map that facilitates the detailed analysis of soil bacteria. This map can be obtained by utilizing 2-DGE to separate genomic DNA fragments produced by polymerase chain reaction (PCR) amplification on the basis of chain length and G+C content. To develop this 2-DGE method further and to apply it to the assessment of bacterial diversity, we carried out a 2-DGE mapping of bacterial DNA fragments from different environmental soils and computed Shannon index as well as plotted rank-abundance curves on the basis of the relative intensity of each spot on the maps. DGGE mapping was also performed to compare the resolution of the two methods. 2-DGE mapping was capable of generating a higher resolution display by a factor of more than 2 using a DGGE fingerprint pattern on a piece of gel. Furthermore, the higher number of detected spots from the 2-DGE map enabled the assessment of differences in bacterial diversity in complex soil systems using a logarithmic normal rank-abundance plot.

Genotypic microbial community profiling: a critical technical review

Microbial ecology has undergone a profound change in the last two decades with regard to methods employed for the analysis of natural communities. Emphasis has shifted from culturing to the analysis of signature molecules including molecular DNA-based approaches that rely either on direct cloning and sequencing of DNA fragments (shotgun cloning) or often rely on prior amplification of target sequences by use of the polymerase chain reaction (PCR). The pool of PCR products can again be either cloned and sequenced or can be subjected to an increasing variety of genetic profiling methods, including amplified ribosomal DNA restriction analysis, automated ribosomal intergenic spacer analysis, terminal restriction fragment length polymorphism, denaturing gradient gel electrophoresis, temperature gradient gel electrophoresis, single strand conformation polymorphism, and denaturing high-performance liquid chromatography. In this document, we present and critically compare these methods commonly used for the study of microbial diversity.

Characterisation of the bacterial flora of modified atmosphere packaged farmed Atlantic cod (Gadus morhua) by PCR-DGGE of conserved 16S rRNA gene regions

The present article describes the use of broad-range molecular analyses to characterise the microbial population of farmed Atlantic cod (Gadus morhua) packaged for the retail market. Cod was filleted post rigor, packaged in air or in modified atmosphere (MA) (50% CO(2):50% N(2) or 50% CO(2):50% O(2)) and stored at 0 degrees C for 11 days. To determine the community profiles of the samples the variable V3-region of the bacterial 16S rRNA gene were amplified by PCR, before the PCR products were separated by denaturing gradient gel electrophoresis (DGGE). From sequence analyses Pseudomonas spp. were found to be the predominant bacteria in oxygen enriched atmospheres, whereas the spoilage bacteria Photobacterium sp., Shewanella putrefaciens and Pseudomonas spp. dominated in CO(2):N(2) and air packaged samples. Additional microbial analyses by cultivation methods observed highest bacterial numbers in air stored samples, and both MA mixtures gave growth inhibition when measuring aerobic plate count, psychrotrophic bacteria and H(2)S-producing bacteria. The results show that PCR-DGGE can be applied to examine bacterial diversity and population shifts among different MA-packaged products.

Large-scale variation in subsurface stream biofilms: a cross-regional comparison of metabolic function and community similarity

We examined bacterial metabolic activity and community similarity in shallow subsurface stream sediments distributed across three regions of the eastern United States to assess whether there were parallel changes in functional and structural attributes at this large scale. Bacterial growth, oxygen consumption, and a suite of extracellular enzyme activities were assayed to describe functional variability. Community similarity was assessed using randomly amplified polymorphic DNA (RAPD) patterns. There were significant differences in streamwater chemistry, metabolic activity, and bacterial growth among regions with, for instance, twofold higher bacterial production in streams near Baltimore, MD, compared to Hubbard Brook, NH. Five of eight extracellular enzymes showed significant differences among regions. Cluster analyses of individual streams by metabolic variables showed clear groups with significant differences in representation of sites from different regions among groups. Clustering of sites based on randomly amplified polymorphic DNA banding resulted in groups with generally less internal similarity although there were still differences in distribution of regional sites. There was a marginally significant (p = 0.09) association between patterns based on functional and structural variables. There were statistically significant but weak (r2 approximately 30%) associations between landcover and measures of both structure and function. These patterns imply a large-scale organization of biofilm communities and this structure may be imposed by factor(s) such as landcover and covariates such as nutrient concentrations, which are known to also cause differences in macrobiota of stream ecosystems.

Can transgenic maize affect soil microbial communities?

The aim of the experiment was to determine if temporal variations of belowground activity reflect the influence of the Cry1Ab protein from transgenic maize on soil bacteria and, hence, on a regulatory change of the microbial community (ability to metabolize sources belonging to different chemical guilds) and/or a change in numerical abundance of their cells. Litter placement is known for its strong influence on the soil decomposer communities. The effects of the addition of crop residues on respiration and catabolic activities of the bacterial community were examined in microcosm experiments. Four cultivars of Zea mays L. of two different isolines (each one including the conventional crop and its Bacillus thuringiensis cultivar) and one control of bulk soil were included in the experimental design. The growth models suggest a dichotomy between soils amended with either conventional or transgenic maize residues. The Cry1Ab protein appeared to influence the composition of the microbial community. The highly enhanced soil respiration observed during the first 72 h after the addition of Bt-maize residues can be interpreted as being related to the presence of the transgenic crop residues. This result was confirmed by agar plate counting, as the averages of the colony-forming units of soils in conventional treatments were about one-third of those treated with transgenic straw. Furthermore, the addition of Bt-maize appeared to induce increased microbial consumption of carbohydrates in BIOLOG EcoPlates. Three weeks after the addition of maize residues to the soils, no differences between the consumption rate of specific chemical guilds by bacteria in soils amended with transgenic maize and bacteria in soils amended with conventional maize were detectable. Reaped crop residues, comparable to post-harvest maize straw (a common practice in current agriculture), rapidly influence the soil bacterial cells at a functional level. Overall, these data support the existence of short Bt-induced ecological shifts in the microbial communities of croplands' soils.

There is a huge number of studies regarding the effects of exposure to transgenic maize pollen on nontarget insects. These concerns are due to the key role of pollinating insects in ecosystem functioning. Many results are highly debated and controversial. However, soil microbes as nontarget organisms are neglected. This is surprising, given the wide variation in agro-ecosystems that arises from several bacterial-driven processes (soil respiration, priming effect of organic matter, litter quality and quantity, and many others). Should the inclusion of bacteria in these nontarget organisms be regarded as artifactual? This seems unambiguous, as soil bacteria themselves are known to be the most crucial element of ecosystem functioning. Effects on the metabolism of soil bacteria grown in microcosms treated with either transgenic or conventional maize straw were studied in the laboratory. In contrast to the authors' expectations, empirical evidence is available to show different utilization of carbon compounds, especially of carbohydrates, according to the concentration of the Bt toxin. To their knowledge, this is the first concrete attempt to address the belowground impact of transgenic maize under controlled situations. The next step must be the assessment of the extent to which bacteria could be endowed with transgenic plant DNA in the soil.

Microbial biogeography: putting microorganisms on the map

We review the biogeography of microorganisms in light of the biogeography of macroorganisms. A large body of research supports the idea that free-living microbial taxa exhibit biogeographic patterns. Current evidence confirms that, as proposed by the Baas-Becking hypothesis, 'the environment selects' and is, in part, responsible for spatial variation in microbial diversity. However, recent studies also dispute the idea that 'everything is everywhere'. We also consider how the processes that generate and maintain biogeographic patterns in macroorganisms could operate in the microbial world.

Confidence intervals of similarity values determined for cloned SSU rRNA genes from environmental samples

The goal of this research was to investigate the influence of the error rate of sequence determination on the differentiation of cloned SSU rRNA gene sequences for assessment of community structure. SSU rRNA cloned sequences from groundwater samples that represent different bacterial divisions were sequenced multiple times with the same sequencing primer. From comparison of sequence alignments with unedited data, confidence intervals were obtained from both a 'double binomial' model of sequence comparison and by non-parametric methods. The results indicated that similarity values below 0.9946 are likely derived from dissimilar sequences at a confidence level of 0.95, and not sequencing errors. The results confirmed that screening by direct sequence determination could be reliably used to differentiate at the species level. However, given sequencing errors comparable to those seen in this study, sequences with similarities above 0.9946 should be treated as the same sequence if a 95% confidence is desired.

The metagenomics of soil

Phylogenetic surveys of soil ecosystems have shown that the number of prokaryotic species found in a single sample exceeds that of known cultured prokaryotes. Soil metagenomics, which comprises isolation of soil DNA and the production and screening of clone libraries, can provide a cultivation-independent assessment of the largely untapped genetic reservoir of soil microbial communities. This approach has already led to the identification of novel biomolecules. However, owing to the complexity and heterogeneity of the biotic and abiotic components of soil ecosystems, the construction and screening of soil-based libraries is difficult and challenging. This review describes how to construct complex libraries from soil samples, and how to use these libraries to unravel functions of soil microbial communities.

Molecular approaches to the assessment of biodiversity in aquatic microbial communities

For the past 20 years, the increased development and routine application of molecular-based techniques has made it possible to carry out detailed evaluations of the biodiversity of aquatic microbial communities. It also offers great opportunities for finding out how this parameter responds to various environmental stresses. Most of these approaches involve an initial PCR amplification of a target, which is generally located within the ribosomal operon. The amplification is achieved by means of primers that are specific to the organisms of interest. The second step involves detecting sequence variations in the PCR fragments either by a cloning/sequencing analysis, which provides a complete characterization of the fragments, or by an electrophoretic analysis, which provides a visual separation of the mixture of fragments according to sequence polymorphism (denaturing or temperature gradient gel electrophoresis, single strand conformation polymorphism) or length polymorphism (terminal-restriction fragment length polymorphism, automated ribosomal intergenic spacer analysis). Other non-PCR-based methods are also commonly used, such as fluorescence in-situ hybridization and DNA re-association analysis. Depending on the technique used, the information gained can be quite different. Moreover, some of these analyses may be rather onerous in terms of time and money, and so not always suitable for screening large numbers of samples. The most widely used techniques are discussed in this paper to illustrate the principles, advantages and shortcomings of each of them. Finally, we will conclude by evaluating the techniques and discussing some emerging molecular techniques, such as real-time PCR and the microarray technique.

Spatial scaling of microbial eukaryote diversity

Patterns in the spatial distribution of organisms provide important information about mechanisms that regulate the diversity of life and the complexity of ecosystems. Although microorganisms may comprise much of the Earth's biodiversity and have critical roles in biogeochemistry and ecosystem functioning, little is known about their spatial diversification. Here we present quantitative estimates of microbial community turnover at local and regional scales using the largest spatially explicit microbial diversity data set available (> 10(6) sample pairs). Turnover rates were small across large geographical distances, of similar magnitude when measured within distinct habitats, and did not increase going from one vegetation type to another. The taxa-area relationship of these terrestrial microbial eukaryotes was relatively flat (slope z = 0.074) and consistent with those reported in aquatic habitats. This suggests that despite high local diversity, microorganisms may have only moderate regional diversity. We show how turnover patterns can be used to project taxa-area relationships up to whole continents. Taxa dissimilarities across continents and between them would strengthen these projections. Such data do not yet exist, but would be feasible to collect.

Methods of studying soil microbial diversity

Soil microorganisms, such as bacteria and fungi, play central roles in soil fertility and promoting plant health. This review examines and compares the various methods used to study microbial diversity in soil.

The soil metagenome – a rich resource for the discovery of novel natural products

Soil microorganisms have been the most valuable source of natural products, providing industrially important antibiotics and biocatalysts. But, of late, the discovery rate of novel biomolecules using traditional cultivation techniques has been extremely low, as most soil microorganisms cannot be cultured in this way. The development of novel cultivation-dependent and molecular cultivation-independent approaches has paved the way for a new era of product recovery from soil microorganisms. In particular, gene-mining based on the construction and screening of complex libraries derived from the soil metagenome provides opportunities to fully explore and exploit the enormous genetic and metabolic diversity of soil microorganisms. This strategy has already resulted in the isolation of novel biocatalysts and bioactive molecules.

Recent advances in petroleum microbiology

Recent advances in molecular biology have extended our understanding of the metabolic processes related to microbial transformation of petroleum hydrocarbons. The physiological responses of microorganisms to the presence of hydrocarbons, including cell surface alterations and adaptive mechanisms for uptake and efflux of these substrates, have been characterized. New molecular techniques have enhanced our ability to investigate the dynamics of microbial communities in petroleum-impacted ecosystems. By establishing conditions which maximize rates and extents of microbial growth, hydrocarbon access, and transformation, highly accelerated and bioreactor-based petroleum waste degradation processes have been implemented. Biofilters capable of removing and biodegrading volatile petroleum contaminants in air streams with short substrate-microbe contact times (<60 s) are being used effectively. Microbes are being injected into partially spent petroleum reservoirs to enhance oil recovery. However, these microbial processes have not exhibited consistent and effective performance, primarily because of our inability to control conditions in the subsurface environment. Microbes may be exploited to break stable oilfield emulsions to produce pipeline quality oil. There is interest in replacing physical oil desulfurization processes with biodesulfurization methods through promotion of selective sulfur removal without degradation of associated carbon moieties. However, since microbes require an environment containing some water, a two-phase oil-water system must be established to optimize contact between the microbes and the hydrocarbon, and such an emulsion is not easily created with viscous crude oil. This challenge may be circumvented by application of the technology to more refined gasoline and diesel substrates, where aqueous-hydrocarbon emulsions are more easily generated. Molecular approaches are being used to broaden the substrate specificity and increase the rates and extents of desulfurization. Bacterial processes are being commercialized for removal of H(2)S and sulfoxides from petrochemical waste streams. Microbes also have potential for use in removal of nitrogen from crude oil leading to reduced nitric oxide emissions provided that technical problems similar to those experienced in biodesulfurization can be solved. Enzymes are being exploited to produce added-value products from petroleum substrates, and bacterial biosensors are being used to analyze petroleum-contaminated environments.