Automated approach for ribosomal intergenic spacer analysis of microbial diversity and its application to freshwater bacterial communities

Copper and zinc isotope fractionation during phototrophic biofilm growth

Copper (Cu) and zinc (Zn) are two trace metals that exhibit both limiting and toxic effects on aquatic microorganisms. However, in contrast to good knowledge of these metal interactions with individual microbial cultures, the biofilm, complex natural consortium of microorganisms, remains poorly understood with respect to its control on Cu and Zn in the aquatic environments. Towards constraining the magnitude and mechanisms of Cu and Zn isotope fractionation in the presence of phototrophic biofilms composed of different proportion of diatoms, green algae and cyanobacteria, we studied long-term growth in a rotating annular bioreactor and quantified the uptake of metals and their isotope fractionation at environmentally-relevant Cu and Zn concentrations. An enrichment of the biofilm in heavy Cu isotope at the beginning of growth suggests the dominance of adsorption processes, followed by intracellular uptake leading to progressive enrichment in light isotope and an excretion of heavy isotope, likely linked to Cu(II) reduction. In the case of Zn, we evidenced only weak isotope fractionation which implies the presence of heavier isotope adsorption (notably in the case of cyanobacteria-dominated biofilm) followed by intracellular incorporation of lighter isotopes. The microbial community plays important role in overall magnitude and even direction of fractionation, suggesting sizable complexity of the processes controlling metal isotope fractionation during phototrophic biofilm growth. However, Cu and Zn isotopes during long-term metal accumulation in riverine biofilm can be used for monitoring the source of environmental pollution in aquatic systems, provided that variations within different sources exceed the natural isotopic fractionation between the biofilm and aqueous solution.

Lessons Learned from the Sea Star Wasting Disease Investigation

Marine invertebrate mass mortality events (MMEs) threaten biodiversity and have the potential to catastrophically alter ecosystem structure. A proximal question around acute MMEs is their etiologies and/or environmental drivers. Establishing a robust cause of mortality is challenging in marine habitats due to the complexity of the interactions among species and the free dispersal of microorganisms from surrounding waters to metazoan microbiomes. The 2013-2014 sea star wasting disease (SSWD) MME in the northeast Pacific Ocean highlights the difficulty in establishing responsible agents. In less than a year of scientific investigation, investigators identified a candidate agent and provided at the time convincing data of pathogenic and transmissible disease. However, later investigation failed to support the initial results, and critical retrospective analyses of experimental procedures and reinterpretation of early findings disbanded any candidate agent. Despite the circuitous path that the investigation and understanding of SSWD have taken, lessons learned from the initial investigation-improving on approaches that led to misinterpretation-have been successfully applied to the 2022 Diadema antillarum investigation. In this review, we outline the history of the initial SSWD investigation, examine how early exploration led to spurious interpretations, summarize the lessons learned, provide recommendations for future work in other systems, and examine potential links between the SSWD event and the Diadema antillarum MME.

Assessment of co-contaminated soil amended by graphene oxide: Effects on pollutants, microbial communities and soil health

Graphene oxide (GOx) is a nanomaterial with demonstrated capacity to remove metals from water. However, its effects on organic pollutants and metal(loid)s present in polluted soils when used for remediation purposes have not been extensively addressed. Likewise, few studies describe the effects of GOx on edaphic properties and soil biology. In this context, here we assessed the potential of GOx for remediating polluted soil focusing also on different unexplored effects of GOx in soil. To achieve this, we treated soil contaminated with concurrent inorganic (As and metals) and organic pollution (TPH and PAHs), using GOx alone and in combination with nutrients (N and P sources). In both cases increased availability of As and Zn was observed after 90 days, whereas Cu and Hg availability was reduced and the availability of Pb and the concentration of organic pollutants were not significantly affected. The application of GOx on the soil induced a significant and rapid change (within 1 week) in microbial populations, leading to a transient reduction in biodiversity, consistent with the alteration of several soil properties. Concurrently, the combination with nutrients exhibited a distinct behaviour, manifesting a more pronounced and persistent shift in microbial populations without a decrease in biodiversity. On the basis of these findings, GOx emerges as a versatile amendment for soil remediation approaches.

Microbial consortia degrade several widely used organic UV filters, but a number of hydrophobic filters remain recalcitrant to biodegradation

Organic UV filters are important ingredients in many personal care products, including sunscreens. Evaluating the biodegradability of organic UV filters is key to estimate their recalcitrance and environmental fate and thus central to their overall environmental risk assessment. In order to further understand the degradation process, the aim was to investigate whether specific consortia could degrade certain UV filters. Several bacterial strains were isolated from enrichment cultures actively degrading octocrylene (OC), butyl methoxydibenzoylmethane (BM), homosalate (HS), and 2-ethylhexyl salicylate (ES) and were utilized to construct an in-house consortium. This synthetic consortium contained 27 bacterial strains and degraded OC, BM, HS, and ES 60-80% after 12 days, but not benzophenone-3 (BP3), methoxyphenyl triazine (BEMT), methylene bis-benzotriazolyl tetramethylbutylphenol (MBBT), diethylhexyl butamido triazone (DBT), ethylhexyl triazone (EHT), or diethylamino hydroxybenzoyl hexyl benzoate (DHHB). Furthermore, several commercial microbial mixtures from Greencell were tested to assess their degradation activity toward the same organic UV filters. ES and HS were degraded by some of the commercial consortia, but to a lesser extent. The rest of the tested UV filters were not degraded by any of the commercial bacterial mixes. These results confirm that some organic UV filters are recalcitrant to biodegradation, while others are degraded by a specific set of microorganisms.

Isolation of Pseudomonas syringae pv. Tomato strains causing bacterial speck disease of tomato and marker-based monitoring for their virulence

BACKGROUND

The bacterial speck disease of tomato caused by a bacterial pathogen Pseudomonas syringae pv. tomato is a most important disease causing severe crop losses.

METHODS AND RESULTS

Present study was conducted to investigate and characterize the population diversity of P. syringae pv. tomato pathogen isolated from infected tomato plants from various regions of Egypt. Significant variation among the isolates was observed which demonstrated considerable virulence. All isolates were pathogenic and the CFU population recovered from inoculate tomato leaves by isolate Pst-2 was higher than other isolates. Genetic disparity among the isolates was investigated by PCR analysis by amplifying hrpZ gene using random amplified polymorphic DNA (RAPD), sequence-related amplified polymorphism (SRAP), and inter-simple sequence repeats (ISSR) markers. The amplified products for ITS1 were found to have 810 bp length whereas 536 bp length was observed for hrpZ gene using primer pairs (1406-f/23S-r) and (MM5-F, MM5-R) respectively. The restriction analysis of amplified regions "ITS" and hrpZ by using 5 and 4 endonucleases respectively demonstrated slight variation among the bacterial isolates. The results of RAPD, ISSR and SRAP showed higher polymorphism (60.52%) within the isolates which may assist for successful characterization by unique and specific markers based on geographical distribution, origin and virulence intensity.

CONCLUSION

The results of present study suggested that the use of molecular approach may provide successful and valuable information to differentiate and classify P. syringae pv. tomato strains in future for the detection and confirmation of pathogenicity.

Optimization of Molecular Methods for Detecting Duckweed-Associated Bacteria

The bacterial colonization dynamics of plants can differ between phylogenetically similar bacterial strains and in the context of complex bacterial communities. Quantitative methods that can resolve closely related bacteria within complex communities can lead to a better understanding of plant-microbe interactions. However, current methods often lack the specificity to differentiate phylogenetically similar bacterial strains. In this study, we describe molecular strategies to study duckweed-associated bacteria. We first systematically optimized a bead-beating protocol to co-isolate nucleic acids simultaneously from duckweed and bacteria. We then developed a generic fingerprinting assay to detect bacteria present in duckweed samples. To detect specific duckweed-bacterium associations, we developed a genomics-based computational pipeline to generate bacterial strain-specific primers. These strain-specific primers differentiated bacterial strains from the same genus and enabled the detection of specific duckweed-bacterium associations present in a community context. Moreover, we used these strain-specific primers to quantify the bacterial colonization of duckweed by normalization to a plant reference gene and revealed differences in colonization levels between strains from the same genus. Lastly, confocal microscopy of inoculated duckweed further supported our PCR results and showed bacterial colonization of the duckweed root-frond interface and root interior. The molecular methods introduced in this work should enable the tracking and quantification of specific plant-microbe associations within plant-microbial communities.

Diversity of Methylobacterium species associated with New Zealand native plants

Methylobacterium species are abundant colonizers of the phyllosphere due to the availability of methanol, a waste product of pectin metabolism during plant cell division. The phyllosphere is an extreme environment, with a landscape that is heterogeneous and continuously changing as the plant grows and is exposed to high levels of ultraviolet irradiation. Geographically, New Zealand (NZ) has been isolated for over a million years, has a biologically diverse flora, and is considered a biodiversity hotspot, with most native plants being endemic. We therefore hypothesize that the phyllosphere of NZ native plants harbor diverse groups of Methylobacterium species. Leaf imprinting using methanol-supplemented agar medium was used to isolate bacteria, and diversity was determined using ARDRA and 16S rRNA gene sequencing. Methylobacterium species were successfully isolated from the phyllosphere of 18 of the 20 native NZ plant species in this study, and six different species were identified: M. marchantiae, M. mesophilicum, M. adhaesivum, M. komagatae, M. extorquens, and M. phyllosphaerae. Other α, β, and γ-Proteobacteria, Actinomycetes, Bacteroidetes, and Firmicutes were also isolated, highlighting the presence of other potentially novel methanol utilizers within this ecosystem. This study identified that Methylobacterium are abundant members of the NZ phyllosphere, with species diversity and composition dependent on plant species.

Effective bioremediation of soil from the Burgan oil field (Kuwait) using compost: A comprehensive hydrocarbon and DNA fingerprinting study

An innovative combination of metagenomic profiling of microbial communities and GC-MS & Pyrolysis-GC-MS fingerprinting methods were used to assess the biodegradation of contaminated soil from the Burgan oil field in Kuwait. The soil was treated with (sludge) compost in microcosms to evaluate the feasibility of this material for bioremediation purposes. The most favourable trial showed a > 80% decrease in TPH, thereby indicating strong potential for full-scale application using a cost-effective technology and thus in line with the principles of the circular economy. The microbial study showed that compost addition enhanced the organic matter and nutrient content of the soil. However, the microorganisms in the compost did not seem to play a relevant role in bioremediation, meaning that compost amendments serve as a biostimulation rather than a bioaugmentation approach. The chemical study of the distinct oil fractions revealed rapidly biodegraded compounds (alkanes, alkyl-aromatics, etc.) and others that were much more refractory (hopanes, benzohopanes, etc.). Of note, although heavy fractions are usually considered recalcitrant to biodegradation, we observed incipient degradation of the asphaltene fraction by means of double-shot thermodesorption and pyrolysis. Finally, chemical fingerprinting also revealed that the treated soil contained some of the compounds found in the compost, such as coprostanol, cholesterol, and plant sterols. This observation would support the use of these compounds as proxies to monitor the effects of compost and to adjust dosages in real-scale bioremediation treatments.

High-resolution phylogenetic and population genetic analysis of microbial communities with RoC-ITS

Microbial communities are inter-connected systems of incredible complexity and dynamism that play crucial roles in health, energy, and the environment. To better understand microbial communities and how they respond to change, it is important to know which microbes are present and their relative abundances at the greatest taxonomic resolution possible. Here, we describe a novel protocol (RoC-ITS) that uses the single-molecule Nanopore sequencing platform to assay the composition of microbial communities at the subspecies designation. Using rolling-circle amplification, this methodology produces long-read sequences from a circular construct containing the complete 16S ribosomal gene and the neighboring internally transcribed spacer (ITS). These long reads can be used to generate a high-fidelity circular consensus sequence. Generally, the ribosomal 16S gene provides phylogenetic information down to the species-level, while the much less conserved ITS region contains strain-level information. When linked together, this combination of markers allows for the identification of individual ribosomal units within a specific organism and the assessment of their relative stoichiometry, as well as the ability to monitor subtle shifts in microbial community composition with a single generic assay. We applied RoC-ITS to an artificial microbial community that was also sequenced using the Illumina platform, to assess its accuracy in quantifying the relative abundance and identity of each species.

Effects of alder- and salmon-derived nutrients on aquatic bacterial community structure and microbial community metabolism in subarctic lakes

Alder (Alnus spp.) and Pacific salmon (Oncorhynchus spp.) provide key nutrient subsidies to freshwater systems. In southwestern Alaska, alder-derived nutrients (ADNs) are increasing as alder cover expands in response to climate warming, while climate change and habitat degradation are reducing marine-derived nutrients (MDNs) in salmon-spawning habitats. To assess the relative influences of ADN and MDN on aquatic microbial community structure and function, we analyzed lake chemistry, bacterial community structure, and microbial metabolism in 13 lakes with varying alder cover and salmon abundance in southwestern Alaska. We conducted bioassays to determine microbial nutrient limitation and physical factors modulating microbial response to nutrient inputs (+N, +P and +NP treatments). Seasonal shifts in bacterial community structure (F = 7.47, P < 0.01) coincided with changes in lake nitrogen (N) and phosphorus (P) concentrations (r² = 0.19 and 0.16, both P < 0.05), and putrescine degradation (r² = 0.13, P = 0.06), suggesting the influx and microbial use of MDN. Higher microbial metabolism occurred in summer than spring, coinciding with salmon runs. Increased microbial metabolism occurred in lakes where more salmon spawned. Microbial metabolic activity was unrelated to alder cover, likely because ADN provides less resource diversity than MDN. When nutrients were added to spring samples, there was greater substrate use by microbial communities from lakes with elevated Chl a concentrations and large relative catchment areas (β estimates for all treatments > 0.56, all P < 0.07). Thus, physical watershed and lake features mediate the effects of nutrient subsidies on aquatic microbial metabolic activity.

Evaluation of the degradation capacity of WWTP sludge enrichment cultures towards several organic UV filters and the isolation of octocrylene-degrading microorganisms

Organic UV filters are present in wastewater treatment plants (WWTPs) due to the use of these compounds in many personal care products (PCPs) and their subsequent release into the wastewater system from showering/bathing. Once in the wastewater system, organic UV filters generally partition into the solid phase but might also undergo other processes, such as degradation by microorganisms. To further understand the fate of organic UV filters in WWTPs, the degradation of 7 UV filters by WWTP sludge was investigated The UV filters 2-ethylhexyl salicylate (ES), homosalate (HS), butyl methoxydibenzoylmethane (BM) and octocrylene (OC) were degraded after 20-60 days. The rest of the filters tested, namely, bis-ethylhexyloxyphenol methoxyphenyl triazine (BEMT), methylene bis-benzotriazolyl tetramethylbutylphenol (MBBT) and diethylhexyl butamido triazone (DBT), did not degrade even after 120 days of incubation. The microbial community from the microcosms degrading ES, HS, OC and BM was transferred every 30 days into new microcosms to enrich for microorganisms capable of utilizing the individual UV filters for growth. The enrichment cultures continued to degrade throughout 20 transfers. The microbial community was clearly different between the enrichments degrading ES, HS, OC and BM, meaning that the microbial community was strongly influenced by the UV filter present. Furthermore, several strains were isolated from OC-degrading cultures and two of these strains, Gordonia sp. strain OC_S5 and Sphingopyxis sp. strain OC_4D, degraded OC with and without other carbon sources present. These experiments show that several organic UV filters can be degraded by a specific set of microorganisms. The lack of degradation observed for BEMT, MBBT and DBT is probably due to limited bioavailability. Indeed, this is the first biodegradation study of these filters, in addition to being the first description of ES and HS degradation in microcosm experiments.

Therapeutic Effects of Modified Tempeh on Glycemic Control and Gut Microbiota Diversity in Diabetic Rats

Background:

The role of the gut microbiota in improving glycemic control in diabetic patients is gaining attention. Tempeh is a fermented soy food from Indonesia that has antidiabetic and antidysbiotic effects. Interestingly, modification of tempeh processing by adding lactic acid bacteria has been reported to enhance the antidiabetic effect of tempeh.

Aim:

To evaluate the effects of modified tempeh on serum glucose, insulin, and gut microbiota diversity of diabetic rats.

Methods:

Modified tempeh was developed by adding lactic acid bacteria from fermented cassava during tempeh processing. Diabetes was induced by injection of streptozotocin nicotinamide. Normal tempeh or modified tempeh was added to the diet and replaced 15% or 30% of casein. Serum glucose and insulin were analyzed before and after 30 days of intervention. At the end of the experiment, the appendix was sampled for gut microbiota analysis.

Result:

Modified tempeh has a significantly higher number of lactic acid bacteria (9.99±0.09 versus 7.74±0.07 log CFU, p < 0.001) compared to normal tempeh. There was a significant difference (p < 0.01) in serum glucose and insulin after treatment. Both tempeh supplements increased the diversity of the gut microbiota. Gut microbiota diversity has a strong negative correlation with delta glucose (r=-0.63, p < 0.001) and delta insulin resistance index (r=-0.54, p=0.003).

Conclusion:

Modified tempeh has potential therapeutic antidiabetic activity, possibly through increased diversity of the gut microbiota.

Control of Fusarium and nematodes by entomopathogenic fungi for organic production of Zingiber officinale

Ginger (genus Zingiber) is widely used as a spice and a medicinal herb worldwide and is the major ingredient of traditional local drinks such as jamu in Southeast Asia. Because ginger is frequently consumed, there is an increasing interest in organic ginger production without the use of synthetic agrochemicals. Recent studies have reported that certain kinds of entomopathogenic fungi (EPF) can establish endophytic- or mycorrhiza-like relationships with plants, thereby promoting plant growth and health, in addition to their typical role in crop protection as biological control agents. In this study, we explored the possibility of non-entomopathogenic effects of EPF Beauveria bassiana and Cordyceps fumosorosea on ginger plants (Zingiber officinale) via antagonism with Fusarium oxysporum or the parasitic nematode Meloidogyne incognita. The two EPF negatively affected the growth of F. oxysporum and survival of M. incognita in vitro. The application of EPF did not have any negative effect on the growth of ginger plants. Soil chemical properties were not different between the plots with or without EPF application, while the diversity of soil bacteria was observed to increase on application of EPF. At least C. fumosorosea appeared to persist in soil during the period of ginger cultivation. Thus, these EPF are potentially useful tools for producing chemical-free ginger.

High-throughput molecular technologies for unraveling the mystery of soil microbial community: challenges and future prospects

Soil microbial communities play a crucial role in soil fertility, sustainability, and plant health. However, intensive agriculture with increasing chemical inputs and changing environments have influenced native soil microbial communities. Approaches have been developed to study the structure, diversity, and activity of soil microbes to better understand the biology and plant-microbe interactions in soils. Unfortunately, a good understanding of soil microbial community remains a challenge due to the complexity of community composition, interactions of the soil environment, and limitations of technologies, especially related to the functionality of some taxa rarely detected using conventional techniques. Culture-based methods have been shown unable and sometimes are biased for assessing soil microbial communities. To gain further knowledge, culture-independent methods relying on direct analysis of nucleic acids, proteins, and lipids are worth exploring. In recent years, metagenomics, metaproteomics, metatranscriptomics, and proteogenomics have been increasingly used in studying microbial ecology. In this review, we examined the importance of microbial community to soil quality, the mystery of rhizosphere and plant-microbe interactions, and the biodiversity and multi-trophic interactions that influence the soil structure and functionality. The impact of the cropping system and climate change on the soil microbial community was also explored. Importantly, progresses in molecular biology, especially in the development of high-throughput biotechnological tools, were extensively assessed for potential uses to decipher the diversity and dynamics of soil microbial communities, with the highlighted advantages/limitations.

The Impact of Disturbed Soil Structure on the Degradation of 2 Fungicides Under Constant and Variable Moisture

Degradation of agrochemicals in soil is frequently faster under field conditions than in laboratory studies. Field studies are carried out on relatively undisturbed soil, whereas laboratory studies typically use sieved soil, which can have a significant impact on the physical and microbial nature of the soil and may contribute to differences in degradation between laboratory and field studies. A laboratory study was therefore conducted to determine the importance of soil structure and variable soil moisture on the degradation of 2 fungicides (azoxystrobin and paclobutrazol) that show significant differences between laboratory and field degradation rates in regulatory studies. Degradation rates were measured in undisturbed cores of a sandy clay loam soil (under constant or variable moisture contents) and in sieved soil. For azoxystrobin, degradation rates under all conditions were similar (median degradation time [DegT50] 34-37 d). However, for paclobutrazol, degradation was significantly faster in undisturbed cores (DegT50 255 d in sieved soil and 63 d in undisturbed cores). Varying the moisture content did not further enhance degradation of either fungicide. Further examination into the impact of soil structure on paclobutrazol degradation, comparing undisturbed and sieved/repacked cores, revealed that the impact of sieving could not be mitigated by repacking the soil to a realistic bulk density. Examination of fungal and bacterial community structure using automated ribosomal spacer analysis showed significant initial differences between sieved/repacked and intact soil cores, although such differences were reduced at the end of the study (70 d). The present study demonstrates that disruption of soil structure significantly impacts microbial community structure, and for some compounds this may explain the differences between laboratory and field degradation rates. Environ Toxicol Chem 2021;40:2715-2725. © 2021 SETAC.

Diversity and Taxonomic Distribution of Endophytic Bacterial Community in the Rice Plant and Its Prospective

Endophytic bacterial communities are beneficial communities for host plants that exist inside the surfaces of plant tissues, and their application improves plant growth. They benefit directly from the host plant by enhancing the nutrient amount of the plant’s intake and influencing the phytohormones, which are responsible for growth promotion and stress. Endophytic bacteria play an important role in plant-growth promotion (PGP) by regulating the indirect mechanism targeting pest and pathogens through hydrolytic enzymes, antibiotics, biocontrol potential, and nutrient restriction for pathogens. To attain these benefits, firstly bacterial communities must be colonized by plant tissues. The nature of colonization can be achieved by using a set of traits, including attachment behavior and motility speed, degradation of plant polymers, and plant defense evasion. The diversity of bacterial endophytes colonization depends on various factors, such as plants’ relationship with environmental factors. Generally, each endophytic bacteria has a wide host range, and they are used as bio-inoculants in the form of synthetic applications for sustainable agriculture systems and to protect the environment from chemical hazards. This review discusses and explores the taxonomic distribution of endophytic bacteria associated with different genotypes of rice plants and their origin, movement, and mechanism of PGP. In addition, this review accentuates compressive meta data of endophytic bacteria communities associated with different genotypes of rice plants, retrieves their plant-growth-promoting properties and their antagonism against plant pathogens, and discusses the indication of endophytic bacterial flora in rice plant tissues using various methods. The future direction deepens the study of novel endophytic bacterial communities and their identification from rice plants through innovative techniques and their application for sustainable agriculture systems.

Volatile Fatty Acid Production from Food Waste Leachate Using Enriched Bacterial Culture and Soil Bacteria as Co-Digester

The production of volatile fatty acids (VFAs) from waste stream has been recently getting attention as a cost-effective and environmentally friendly approach in mechanical–biological treatment plants. This is the first study to explore the use of a functional bacterium, AM5 isolated from forest soil, which is capable of enhancing the production of VFAs in the presence of soil bacteria as a co-digester in non-strict anaerobic fermentation processes of food waste leachates. Batch laboratory-scale trials were conducted under thermophilic conditions at 55 °C and different pH values ranging from approximately 5 to 11, as well as under uncontrolled pH for 15 days. Total solid content (TS) and volatile solid content (VS) were observed with 58.42% and 65.17% removal, respectively. An effluent with a VFA concentration of up to 33,849 mg/L (2365.57 mg/g VS; 2244.45 mg/g chemical oxygen demand (COD)-VFA VS; 1249 mg/g VSremoved) was obtained at pH 10.5 on the second day of the batch culture. The pH resulted in a significant effect on VFA concentration and composition at various values. Additionally, all types of VFAs were produced under pH no-adjustment (approximately 5) and at pH 10.5. This research might lead to interesting questions and ideas for further studies on the complex metabolic pathways of microbial communities in the mixture of a soil solution and food waste leachate.

Characterisation of Environmental Biofilms Colonising Wall Paintings of the Fornelle Cave in the Archaeological Site of Cales

Caves present unique habitats for the development of microbial communities due to their peculiar environmental conditions. In caves decorated with frescoes, the characterization of microbial biofilm is important to better preserve and safeguard such artworks. This study aims to investigate the microbial communities present in the Fornelle Cave (Calvi Risorta, Caserta, Italy) and their correlation with environmental parameters. The cave walls and the wall paintings have been altered by environmental conditions and microbial activity. We first used light microscopy and scanning electron microscopy (SEM) and X-ray diffraction to characterise the biofilm structure and the mineral composition of substrata, respectively. Then, using both culture-dependent (Sanger sequencing) and culture-independent (automated ribosomal intergenic spacer analysis, ARISA) molecular methods, we demonstrated that the taxonomic composition of biofilms was different across the three substrata analysed and, in some cases, positively correlated with some environmental parameters. We identified 47 taxa in the biofilm samples, specifically 8 bacterial, 18 cyanobacterial, 14 algal and 7 fungal taxa. Fungi showed the highest number of ARISA types on the tuff rock, while autotrophic organisms (cyanobacteria and algae) on the frescoes exposed to light. This study confirms that caves constitute a biodiversity-rich environment for microbial taxa and that, in the presence of wall paintings, taxonomic characterization is particularly important for conservation and restoration purposes.

The microbial rare biosphere: current concepts, methods and ecological principles

Our ability to describe the highly diverse pool of low abundance populations present in natural microbial communities is increasing at an unprecedented pace. Yet we currently lack an integrative view of the key taxa, functions and metabolic activity which make-up this communal pool, usually referred to as the 'rare biosphere', across the domains of life. In this context, this review examines the microbial rare biosphere in its broader sense, providing an historical perspective on representative studies which enabled to bridge the concept from macroecology to microbial ecology. It then addresses our current knowledge of the prokaryotic rare biosphere, and covers emerging insights into the ecology, taxonomy and evolution of low abundance microeukaryotic, viral and host-associated communities. We also review recent methodological advances and provide a synthetic overview on how the rare biosphere fits into different conceptual models used to explain microbial community assembly mechanisms, composition and function.

Microbial Succession under Freeze-Thaw Events and Its Potential for Hydrocarbon Degradation in Nutrient-Amended Antarctic Soil

The polar regions have relatively low richness and diversity of plants and animals, and the basis of the entire ecological chain is supported by microbial diversity. In these regions, understanding the microbial response against environmental factors and anthropogenic disturbances is essential to understand patterns better, prevent isolated events, and apply biotechnology strategies. The Antarctic continent has been increasingly affected by anthropogenic contamination, and its constant temperature fluctuations limit the application of clean recovery strategies, such as bioremediation. We evaluated the bacterial response in oil-contaminated soil through a nutrient-amended microcosm experiment using two temperature regimes: (i) 4 °C and (ii) a freeze–thaw cycle (FTC) alternating between −20 and 4 °C. Bacterial taxa, such as Myxococcales, Chitinophagaceae, and Acidimicrobiales, were strongly related to the FTC. Rhodococcus was positively related to contaminated soils and further stimulated under FTC conditions. Additionally, the nutrient-amended treatment under the FTC regime enhanced bacterial groups with known biodegradation potential and was efficient in removing hydrocarbons of diesel oil. The experimental design, rates of bacterial succession, and level of hydrocarbon transformation can be considered as a baseline for further studies aimed at improving bioremediation strategies in environments affected by FTC regimes.

Efficient degradation of the organic UV filter benzophenone-3 by Sphingomonas wittichii strain BP14P isolated from WWTP sludge

Benzophenone-3 (BP3) is a widely used organic UV filter present in many environmental compartments. One way BP3 is released into the environment is through effluents from wastewater treatment plants (WWTPs). These plants are possible sources for degradation activity and WWTP sludge may potentially degrade BP3. Our goal was to identify any BP3 degrading microorganism(s) in WWTP sludge and to investigate whether the degradation was co-metabolic. Initial WWTP sludge microcosms spiked with BP3 showed 100% degradation after 20 days. Multiple transfers of these microcosms, while maintaining a strong selective pressure for BP3 degradation capabilities, resulted in the dominance of one bacterial strain. This strain was identified as Sphingomonas wittichii BP14P and was subsequently isolated. It was shown to degrade BP3 in a growth dependent manner. Strain BP14P utilized BP3 as the sole energy and carbon source and completely degraded BP3 after 7 days in minimal media. We tested the capability of BP14P to degrade nine other UV filters, but the degradation ability seemed to be restricted to BP3. However, whether this specificity is due to the lack of degradation genes, cellular transport or low bioavailability of the other UV filters remained unclear. The efficient degradation of BP3 by a group of bacteria well known for their potential for xenobiotic degradation is an important step forward for a complete risk assessment of the long-term environmental impact of BP3.

Impact of cigarette butts on bacterial community structure in soil

Cigarette butts contribute significantly to global pollution present on the planet. The filters found in cigarette butts contain a microplastic, cellulose acetate, as well as toxic metals and metalloids which are responsible for pollution in the environment. Although cigarette butt litter is prevalent in many soils, research on the effects of these cigarette butts is limited. In this study, we used Automated Ribosomal Intergenic Spacer Analysis (ARISA) to generate DNA fingerprints of bacterial communities in soil before and after the addition of cigarette butt leachate treatments. An ICP-MS analysis of the biodegradable and non-biodegradable cigarette butts revealed the presence of various elements: Al, As, B, Ba, Cd, Co, Cr, Cu, Fe, Hg, Mn, Mo, Ni, Pb, Sb, Se, Sn, Sr, V, and Zn. The analysis also specified which metals were present at the highest concentrations in the biodegradable and non-biodegradable cigarette butts, and these were, respectively, Al (1,31 g/kg and 2,35 g/kg), Fe (2,03 g/kg and 1,11 g/kg), and Zn (3,18 mg/kg and 15,70 mg/kg). Our results show that biodegradable cigarette butts had a significant effect on bacterial community composition (beta diversity), unlike the non-biodegradable butts. This effect can be attributed to higher concentrations of certain metals and metalloids in the leachate of biodegradable cigarette butts compared to the non-biodegradable ones. Our findings suggest that biodegradable and non-biodegradable cigarette butts can significantly affect bacterial communities in soil as a result of the leaching of significant quantities of certain elements into the surrounding soils.

Microdiversity and phylogeographic diversification of bacterioplankton in pelagic freshwater systems revealed through long-read amplicon sequencing

BACKGROUND

Freshwater ecosystems are inhabited by members of cosmopolitan bacterioplankton lineages despite the disconnected nature of these habitats. The lineages are delineated based on > 97% 16S rRNA gene sequence similarity, but their intra-lineage microdiversity and phylogeography, which are key to understanding the eco-evolutional processes behind their ubiquity, remain unresolved. Here, we applied long-read amplicon sequencing targeting nearly full-length 16S rRNA genes and the adjacent ribosomal internal transcribed spacer sequences to reveal the intra-lineage diversities of pelagic bacterioplankton assemblages in 11 deep freshwater lakes in Japan and Europe.

RESULTS

Our single nucleotide-resolved analysis, which was validated using shotgun metagenomic sequencing, uncovered 7-101 amplicon sequence variants for each of the 11 predominant bacterial lineages and demonstrated sympatric, allopatric, and temporal microdiversities that could not be resolved through conventional approaches. Clusters of samples with similar intra-lineage population compositions were identified, which consistently supported genetic isolation between Japan and Europe. At a regional scale (up to hundreds of kilometers), dispersal between lakes was unlikely to be a limiting factor, and environmental factors or genetic drift were potential determinants of population composition. The extent of microdiversification varied among lineages, suggesting that highly diversified lineages (e.g., Iluma-A2 and acI-A1) achieve their ubiquity by containing a consortium of genotypes specific to each habitat, while less diversified lineages (e.g., CL500-11) may be ubiquitous due to a small number of widespread genotypes. The lowest extent of intra-lineage diversification was observed among the dominant hypolimnion-specific lineage (CL500-11), suggesting that their dispersal among lakes is not limited despite the hypolimnion being a more isolated habitat than the epilimnion.

CONCLUSIONS

Our novel approach complemented the limited resolution of short-read amplicon sequencing and limited sensitivity of the metagenome assembly-based approach, and highlighted the complex ecological processes underlying the ubiquity of freshwater bacterioplankton lineages. To fully exploit the performance of the method, its relatively low read throughput is the major bottleneck to be overcome in the future. Video abstract.

Methods to Identify Soil Microbial Bioindicators of Sustainable Management of Bioenergy Crops

Here we describe a suite of methods to identify potential taxonomic and functional soil microbial indicators of soil quality and plant health in biofuel crops in various areas and land types. This approach draws on tools to assess microbial diversity, greenhouse gas fluxes, and soil physicochemical properties in bioenergy cropping systems. Integrative statistical models are then used to identify potential microbial indicators for sustainable management of bioenergy crops.

Flexible feeding in anaerobic digestion - Impact on process stability, performance and microbial community structures

Biogas has the potential to contribute to some of the most urgent issues of the energy transition, including mobility, energy storage, and grid stability. Flexibilization has been discussed as a means to improve the economics of biogas production, ideally restricting the production of electricity to times of strong need. Here the possibility of demand-driven, flexible biogas production is investigated, which saves substrates and storage capacity, while still enabling control over the production of electricity. Effects of different flexible feeding regimes were tested in a continuously operated 200 L reactor. After a period of 300 days under steady conditions (6.4 kg feed m^-3d^-1), varying flexible feeding patterns were applied over the next 700 days. Biogas production, volatile organic acid concentrations, and microbial dynamics were documented. Reduction of feeding resulted in reducing the gas production by up to 80% within a day. By increasing the feed, gas production could rapidly be reinitiated at similar levels as before even after fasting periods of up to 22 days. CH₄-contents of the produced biogas were nearly constant over the investigation period. As a response to the flexible feeding, a reorganization of the microbial community was observed, which came to an end after 800 days and then was no longer affected by further changes in the feeding patterns or the substrate composition. Dominating archaea were of the order Methanosarcinales. During the experiment, representatives from the class Methanosaetaceae replaced representatives from the class Methanosarcinaceae.

Molecular Methods as Potential Tools in Ecohydrological Studies on Emerging Contaminants in Freshwater Ecosystems

Contaminants of emerging concern (CECs) present a threat to the functioning of freshwater ecosystems. Their spread in the environment can affect both plant and animal health. Ecohydrology serves as a solution for assessment approaches (i.e., threat identification, ecotoxicological assessment, and cause–effect relationship analysis) and solution approaches (i.e., the elaboration of nature-based solutions: NBSs), mitigating the toxic effect of CECs. However, the wide array of potential molecular analyses are not fully exploited in ecohydrological research. Although the number of publications considering the application of molecular tools in freshwater studies has been steadily growing, no paper has reviewed the most prominent studies on the potential use of molecular technologies in ecohydrology. Therefore, the present article examines the role of molecular methods and novel omics technologies as essential tools in the ecohydrological approach to CECs management in freshwater ecosystems. It considers DNA, RNA and protein-level analyses intended to provide an overall view on the response of organisms to stress factors. This is compliant with the principles of ecohydrology, which emphasize the importance of multiple indicator measurements and correlation analysis in order to determine the effects of contaminants, their interaction with other environmental factors and their removal using NBS in freshwater ecosystems.

Application of molecular techniques in biohydrogen production as a clean fuel

Considering the future energy demand and pollution to the environment, biohydrogen, a biofuel, produced from biological sources have garnered increased attention. The present review emphasis the various techniques and methods employed to enumerate the microbial community and enhancement of hydrogen production by dark fermentation. Notably, molecular techniques such as terminal restriction fragment length polymorphism (T-RFLP), quantitative real-time PCR (q-PCR), fluorescent in-situ hybridization (FISH), denaturing gradient gel electrophoresis (DGGE), ribosomal intergenic spacer analysis (RISA), and next generation sequencing (NGS) have been extensively discussed on identifying the microbial population in hydrogen production. Further, challenges and merits of the molecular techniques have been elaborated.

Sediment Microbial Diversity in Urban Piedmont North Carolina Watersheds Receiving Wastewater Input

Urban streams are heavily influenced by human activity. One way that this occurs is through the reintroduction of treated effluent from wastewater treatment plants. We measured the microbial community composition of water, sediment, and soil at sites upstream and downstream from two Charlotte treatment facilities. We performed 16S rRNA gene sequencing to assay the microbial community composition at each site at four time points between the late winter and mid-summer of 2016. Despite the location of these streams in an urban area with many influences and disruptions, the streams maintain distinct water, sediment, and soil microbial profiles. While there is an overlap of microbial species in upstream and downstream sites, there are several taxa that differentiate these sites. Some taxa characteristics of human-associated microbial communities appear elevated in the downstream sediment communities. In the wastewater treatment plant and to a lesser extent in the downstream community, there are high abundance amplicon sequence variants (ASVs) which are less than 97% similar to any sequence in reference databases, suggesting that these environments contain an unexplored biological novelty. Taken together, these results suggest a need to more fully characterize the microbial communities associated with urban streams, and to integrate information about microbial community composition with mechanistic models.

Global warming shifts the composition of the abundant bacterial phyllosphere microbiota as indicated by a cultivation-dependent and -independent study of the grassland phyllosphere of a long-term warming field experiment

The leaf-colonizing bacterial microbiota was studied in a long-term warming experiment on a permanent grassland, which had been continuously exposed to increased surface temperature (+2°C) for more than six years. Two abundant plant species, Arrhenatherum elatius and Galium album, were studied. Surface warming reduced stomata opening and changed leaf metabolite profiles. Leaf surface colonization and the concentration of leaf-associated bacterial cells were not affected. However, bacterial 16S ribosomal RNA (rRNA) gene amplicon Illumina sequencing showed significant temperature effects on the plant species-specific phyllosphere microbiota. Warming partially affected the concentrations of cultured bacteria and had a significant effect on the composition of most abundant cultured plant species-specific bacteria. The abundance of Sphingomonas was significantly reduced. Sphingomonas isolates from warmed plots represented different phylotypes, had different physiological traits and were better adapted to higher temperatures. Among Methylobacterium isolates, a novel phylotype with a specific mxaFtype was cultured from plants of warmed plots while the most abundant phylotype cultured from control plots was strongly reduced. This study clearly showed a correlation of long-term surface warming with changes in the plant physiology and the development of a physiologically and genetically adapted phyllosphere microbiota.

Impact of solid residence time (SRT) on functionally relevant microbial populations and performance in full-scale enhanced biological phosphorus removal (EBPR) systems

Investigations of the impact of solid residence time (SRT) on microbial ecology and performance of enhanced biological phosphorus removal (EBPR) process in full-scale systems have been scarce due to the challenges in isolating and examining the SRT from other complex plant-specific factors. This study performed a comprehensive evaluation of the influence of SRT on polyphosphate-accumulating organisms (PAOs) and glycogen-accumulating organisms (GAOs) dynamics and on P removal performance at Clark County Water Reclamation District Facility in Las Vegas, USA. Five parallel treatment trains with separated clarifiers were operated with five different SRTs ranging from 6 to 40 days. Microbial community analysis using multiple molecular and Raman techniques suggested that the relative abundances and diversity of PAOs and GAOs in EBPR systems are highly affected by the SRT. The resultant EBPR system stability and performance can be potentially controlled and optimized by manipulating the system SRT, and shorter SRT (<10 days) seems to be preferred. PRACTITIONER POINTS: Phosphorus removal performance and kinetics are highly affected by the operational solid residence time (SRT), with lower and more stable effluent P level achieved at SRT < 10 days. Excessive long SRTs above that needed for nitrification may harm EBPR performance; additionally, excessive long SRT may favor GAOs to dominate over PAOs and thus further reducing efficient use of rbCOD for EBPR. Microbial population abundance and diversity, especially those functionally relevant PAOs and GAOs, can impact the P removal performances, and they are highly dependent on the operational solid residence time. EBPR performance can be potentially controlled and optimized by manipulating the system SRT, and shorter SRT (≤10 days) seems to be preferred at the influent rbCOD/P ratio and environmental conditions as in the plant studied.

Microbial community analysis using high-throughput sequencing technology: a beginner's guide for microbiologists

Microbial communities present in diverse environments from deep seas to human body niches play significant roles in the complex ecosystem and human health. Characterizing their structural and functional diversities is indispensable, and many approaches, such as microscopic observation, DNA fingerprinting, and PCR-based marker gene analysis, have been successfully applied to identify microorganisms. Since the revolutionary improvement of DNA sequencing technologies, direct and high-throughput analysis of genomic DNA from a whole environmental community without prior cultivation has become the mainstream approach, overcoming the constraints of the classical approaches. Here, we first briefly review the history of environmental DNA analysis applications with a focus on profiling the taxonomic composition and functional potentials of microbial communities. To this end, we aim to introduce the shotgun metagenomic sequencing (SMS) approach, which is used for the untargeted ("shotgun") sequencing of all ("meta") microbial genomes ("genomic") present in a sample. SMS data analyses are performed in silico using various software programs; however, in silico analysis is typically regarded as a burden on wet-lab experimental microbiologists. Therefore, in this review, we present microbiologists who are unfamiliar with in silico analyses with a basic and practical SMS data analysis protocol. This protocol covers all the bioinformatics processes of the SMS analysis in terms of data preprocessing, taxonomic profiling, functional annotation, and visualization.

Variation in gut bacterial composition is associated with Haemonchus contortus parasite infection of sheep

Background

One of the greatest impediments to global small ruminant production is infection with the gastrointestinal parasite, Haemonchus contortus. In recent years there has been considerable interest in the gut microbiota and its impact on health. Relatively little is known about interactions between the gut microbiota and gastrointestinal tract pathogens in sheep. Thus, this study was undertaken to investigate the link between the faecal microbiota of sheep, as a sample representing the gastrointestinal microbiota, and infection with H. contortus.

Results

Sheep (n = 28) were experimentally inoculated with 14,000 H. contortus infective larvae. Faecal samples were collected 4 weeks prior to and 4 weeks after infection. Microbial analyses were conducted using automated ribosomal intergenic spacer analysis (ARISA) and 16S rRNA gene sequencing. A comparison of pre-infection microbiota to post-infection microbiota was conducted. A high parasite burden associated with a relatively large change in community composition, including significant (p ≤ 0.001) differences in the relative abundances of Firmicutes and Bacteroidetes following infection. In comparison, low parasite burden associated with a smaller change in community composition, with the relative abundances of the most abundant phyla remaining stable. Interestingly, differences were observed in pre-infection faecal microbiota in sheep that went on to develop a high burden of H. contortus infection (n = 5) to sheep that developed a low burden of infection (n = 5). Differences observed at the community level and also at the taxa level, where significant (p ≤ 0.001) in relative abundance of Bacteroidetes (higher in high parasite burden sheep) and Firmicutes (lower in high parasite burden sheep).

Conclusions

This study reveals associations between faecal microbiota and high or low H. contortus infection in sheep. Further investigation is warranted to investigate causality and the impact of microbiome manipulation.

The Impact of Metal-Rich Sediments Derived from Mining on Freshwater Stream Life

Metal-rich sediments have the potential to impair life in freshwater streams and rivers and, thereby, to inhibit recovery of ecological conditions after any remediation of mine water discharges. Sediments remain metal-rich over long time periods and have long-term potential ecotoxicological interactions with local biota, unless the sediments themselves are physically removed or replaced by less metal-rich sediment. Laboratory-derived environmental quality standards are difficult to apply to the field situation, as many complicating factors exist in the real world. Therefore, there is a strong case to consider other, field-relevant, measures of toxic effects as alternatives to laboratory-derived standards and to seek better biological tools to detect, diagnose and ideally predict community-level ecotoxicological impairment. Hence, this review concentrated on field measures of toxic effects of metal-rich sediment in freshwater streams, with less emphasis on laboratory-based toxicity testing approaches. To this end, this review provides an overview of the impact of metal-rich sediments on freshwater stream life, focusing on biological impacts linked to metal contamination.

Bacterial and Fungal Communities Are Differentially Modified by Melatonin in Agricultural Soils Under Abiotic Stress

An extensive body of evidence from the last decade has indicated that melatonin enhances plant resistance to a range of biotic and abiotic stressors. This has led to an interest in the application of melatonin in agriculture to reduce negative physiological effects from environmental stresses that affect yield and crop quality. However, there are no reports regarding the effects of melatonin on soil microbial communities under abiotic stress, despite the importance of microbes for plant root health and function. Three agricultural soils associated with different land usage histories (pasture, canola or wheat) were placed under abiotic stress by cadmium (100 or 280 mg kg-1 soil) or salt (4 or 7 g kg-1 soil) and treated with melatonin (0.2 and 4 mg kg-1 soil). Automated Ribosomal Intergenic Spacer Analysis (ARISA) was used to generate Operational Taxonomic Units (OTU) for microbial community analysis in each soil. Significant differences in richness (α diversity) and community structures (β diversity) were observed between bacterial and fungal assemblages across all three soils, demonstrating the effect of melatonin on soil microbial communities under abiotic stress. The analysis also indicated that the microbial response to melatonin is governed by the type of soil and history. The effects of melatonin on soil microbes need to be regarded in potential future agricultural applications.

Physiological responses of three mono-species phototrophic biofilms exposed to copper and zinc

In freshwater ecosystem, phototrophic biofilms play a crucial role through adsorption and sequestration of organic and inorganic pollutants. However, extracellular polymeric substance (EPS) secretion by phototrophic biofilms exposed to metals is poorly documented. This work evaluated the physiological responses of phototrophic biofilms by exposing three microorganisms (cyanobacterium Phormidium autumnale, diatom Nitzschia palea and green alga Uronema confervicolum) to 20 and 200 μg L^-1 of Cu or 60 and 600 μg L^-1 of Zn, both individually and in combination. Analysis of metal effects on algal biomass and photosynthetic efficiency showed that metals were toxic at higher concentrations for these two parameters together and that all the strains were more sensitive to Cu than to Zn. U. confervicolum was the most impacted in terms of growth, while P. autumnale was the most impacted in terms of photosynthetic efficiency. In consequence to metal exposure at higher concentrations (Cu200, Zn600 and Cu200Zn600), a higher EPS production was measured in diatom and cyanobacterium biofilms, essentially caused by an overproduction of protein-like polymers. On the other hand, the amount of secreted polysaccharides decreased during metal exposure of the diatom and green alga biofilms. Size exclusion chromatography revealed specific EPS molecular fingerprints in P. autumnale and N. palea biofilms that have secreted different protein-like polymers during their development in the presence of Zn600. These proteins were not detected in the presence of Cu200 despite an increase of proteins in the EPS extracts compared to the control. These results highlight interesting divergent responses between the three mono-species biofilms and suggest that increasing protein production in EPS biofilms may be a fingerprint of natural biofilm against metal pollutants in freshwater rivers.

Arsenic metabolism in technical biogas plants: possible consequences for resident microbiota and downstream units

The metal(loid) and in particular the Arsenic (As) burden of thirteen agricultural biogas plants and two sewage sludge digesters were investigated together with the corresponding microbial consortia. The latter were characterized by ARISA (automated ribosomal intergenetic spacer analysis) and next generation sequencing. The consortia were found to cluster according to digester type rather than substrate or metal(loid) composition. For selected plants, individual As species in the liquid and gaseous phases were quantified, showing that the microorganisms actively metabolize and thereby remove the As from their environment via the formation of (methylated) volatile species. The As metabolites showed some dependency on the microbial consortia, while there was no statistical correlation with the substrate mix. Finally, slurry from one agricultural biogas plant and one sewage sludge digester was transferred into laboratory scale reactors ("satellite reactors") and the response to a defined addition of As (30 and 60 µM sodium arsenite) was studied. The results corroborate the hypothesis of a rapid conversion of dissolved As species into volatile ones. Methanogenesis was reduced during that time, while there was no discernable toxic effect on the microbial population. However, the utilization of the produced biogas as replacement for natural gas, e.g. as fuel, may be problematic, as catalysts and machinery are known to suffer from prolonged exposure even to low As concentrations.

The composition and stability of the faecal microbiota of Merino sheep

AIMS

To determine the composition and temporal stability of the gut (faecal) microbiota of sheep (Ovis aries).

METHODS AND RESULTS

Microbial population dynamics was conducted using ARISA (28 sheep) and 16S rRNA sequencing (11 sheep). Firmicutes and Bacteroidetes were the predominant bacterial phyla, constituting ~80% of the total population. The core faecal bacterial microbiota of sheep consisted of 67 of 136 detected families and 91 of 215 detected species. Predominant microbial taxa included Ruminococcaceae, unassigned families in Bacteroidales and Clostridiales, Verrucomicrobiaceae and Paraprevotellaceae. Diversity indices and core microbiota composition demonstrated the stability of the core microbiota over 2-4 weeks. The core microbiota remained similar over ~5 months.

CONCLUSIONS

Temporal stability of the sheep microbiota is high over 2-4 weeks in the absence of experimental variables. The core microbiota of Merino sheep shares taxa found in other breeds of sheep and other ruminants.

SIGNIFICANCE AND IMPACT OF THE STUDY

Numerous studies seek to investigate the impact of experimental variables on gut microbiota composition. To do so, knowledge of the innate stability (or instability) of the microbiota over an experimental time course is required, independent of other variables. We have demonstrated high stability of the gut microbiota in sheep over 3-4 weeks, with moderate stability over ~5 months.

Assessment of prokaryote to eukaryote ratios in environmental samples by SSU rDNA length polymorphism

Microbial communities are important regulators of many processes in all ecosystems. Understanding of ecosystem processes requires at least an overview of the involved microorganisms. While in-depth identification of microbial species in environmental samples can be achieved by next generation sequencing, profiling of whole microbial communities can be accomplished via less labour-intensive approaches. Especially automated ribosomal intergenic spacer analysis (ARISA) are of interest as they are highly specific even at fine scales and widely applicable for environmental samples. Yet, established protocols lack the possibility to compare prokaryotic and eukaryotic communities as different primer sets are necessary. However, shifts in the eukaryote to prokaryote ratio can be a useful indicator for ecosystem processes like decomposition or nutrient cycling. We propose a protocol to analyse prokaryotic and eukaryotic communities using a single primer pair based reaction based on a region with variable length (V4, which is about 180 bp shorter in prokaryotes compared to eukaryotes) in the small ribosomal subunit flanked by two highly conservative regions. Shifts in the prokaryotic and eukaryotic ratio between samples can be reliably detected by fragment length polymorphism analysis as well as sequencing of this region. Together with established approaches such as ARISA or 16S and ITS rDNA sequencing, this can provide a more complex insight into microbial community shifts and ecosystem processes.

The honey bee gut microbiota: strategies for study and characterization

Gut microbiota research is an emerging field that improves our understanding of the ecological and functional dynamics of gut environments. The honey bee gut microbiota is a highly rewarding community to study, as honey bees are critical pollinators of many crops for human consumption and produce valuable commodities such as honey and wax. Most significantly, unique characteristics of the Apis mellifera gut habitat make it a valuable model system. This review discusses methods and pipelines used in the study of the gut microbiota of Ap. mellifera and closely related species for four main purposes: identifying microbiota taxonomy, characterizing microbiota genomes (microbiome), characterizing microbiota-microbiota interactions and identifying functions of the microbial community in the gut. The purpose of this contribution is to increase understanding of honey bee gut microbiota, to facilitate bee microbiota and microbiome research in general and to aid design of future experiments in this growing field.

Bacterial and ciliate biofilm community structure at different spatial levels of a salt lake meta-community

Meta-communities are assembled along an ecological scale that determines local and regional diversity. Spatial patterns have been detected in planktonic bacterial communities at distances <20 m, but little is known about the occurrence of similar variation for other microbial groups and changes in microbial meta-community assembly at different levels of a meta-community. To examine this variation, the biofilm of eight saline ponds were used to investigate processes shaping diversity within ponds (β) and between ponds (δ). Bacterial and ciliate communities were assessed using ARISA and T-RFLP respectively, while diversity partitioning methods were used to examine the importance of taxonomic turnover and variation partitioning was used to distinguish spatial from environmental determinants. The results show that turnover is important for determining β- and δ-diversity of biofilms. Spatial factors are important drivers of bacterial β-diversity but were unimportant for ciliate β-diversity. Environmental variation was a strong determinant of bacterial and ciliate δ-diversity, suggesting sorting processes are important for assembling pond communities. Determinants of diversity in bacteria are not universal for ciliates, suggesting higher functional redundancy of bacteria or the greater niche breadth of ciliates may be important in discriminating assembly processes between the two organisms.

A 16S rDNA PCR-based theoretical to actual delta approach on culturable mock communities revealed severe losses of diversity information

BACKGROUND

Subunits of ribosomal RNA genes (rDNAs) characterized by PCR-based protocols have been the proxy for studies in microbial taxonomy, phylogenetics, evolution and ecology. However, relevant factors have shown to interfere in the experimental outputs in a variety of systems. In this work, a 'theoretical' to 'actual' delta approach was applied to data on culturable mock bacterial communities (MBCs) to study the levels of losses in operational taxonomic units (OTUs) detectability. Computational and lab-bench strategies based on 16S rDNA amplification by 799F and U1492R primers were employed, using a fingerprinting method with highly improved detectability of fragments as a case-study tool. MBCs were of two major types: in silico MBCs, assembled with database-retrieved sequences, and in vitro MBCs, with AluI digestions of PCR data generated from culturable endophytes isolated from cacao trees.

RESULTS

Interfering factors for the 16 s rDNA amplifications, such as the type of template, direct and nested PCR, proportion of chloroplast DNA from a tropical plant source (Virola officinalis), and biased-amplification by the primers resulted in altered bacterial 16S rDNA amplification, both on MBCs and V. officinalis leaf-extracted DNA. For the theoretical data, the maximum number of fragments for in silico and in vitro cuts were not significantly different from each other. Primers' preferences for certain sequences were detected, depending on the MBCs' composition prior to PCR. The results indicated overall losses from 2.3 up to 8.2 times in the number of OTUs detected from actual AluI digestions of MBCs when compared to in silico and in vitro theoretical data.

CONCLUSIONS

Due to all those effects, the final amplification profile of the bacterial community assembled was remarkably simplified when compared to the expected number of detectable fragments known to be present in the MBC. From these findings, the scope of hypotheses generation and conclusions from experiments based on PCR amplifications of bacterial communities was discussed.

Invited review: Plant polyphenols and rumen microbiota responsible for fatty acid biohydrogenation, fiber digestion, and methane emission: Experimental evidence and methodological approaches

The interest of the scientific community in the effects of plant polyphenols on animal nutrition is increasing. These compounds, in fact, are ubiquitous in the plant kingdom, especially in some spontaneous plants exploited as feeding resources alternative to cultivated crops and in several agro-industry by-products. Polyphenols interact with rumen microbiota, affecting carbohydrate fermentation, protein degradation, and lipid metabolism. Some of these aspects have been largely reviewed, especially for tannins; however, less information is available about the direct effect of polyphenols on the composition of rumen microbiota. In the present paper, we review the most recent literature about the effect of plant polyphenols on rumen microbiota responsible for unsaturated fatty acid biohydrogenation, fiber digestion, and methane production, taking into consideration the advances in microbiota analysis achieved in the last 10 yr. Key aspects, such as sample collection, sample storage, DNA extraction, and the main phylogenetic markers used in the reconstruction of microbial community structure, are examined. Furthermore, a summary of the new high-throughput methods based on next generation sequencing is reviewed. Several effects can be associated with dietary polyphenols. Polyphenols are able to depress or modulate the biohydrogenation of unsaturated fatty acids by a perturbation of ruminal microbiota composition. In particular, condensed tannins have an inhibitory effect on biohydrogenation, whereas hydrolyzable tannins seem to have a modulatory effect on biohydrogenation. With regard to fiber digestion, data from literature are quite consistent about a general depressive effect of polyphenols on gram-positive fibrolytic bacteria and ciliate protozoa, resulting in a reduction of volatile fatty acid production (mostly acetate molar production). Methane production is also usually reduced when tannins are included in the diet of ruminants, probably as a consequence of the inhibition of fiber digestion. However, some evidence suggests that hydrolyzable tannins may reduce methane emission by directly interacting with rumen microbiota without affecting fiber digestion.

Bioremediation of bezafibrate and paroxetine by microorganisms from estuarine sediment and activated sludge of an associated wastewater treatment plant

The present work aimed to explore the potential of autochthonous microorganisms from an urban estuary and from activated sludge of an associated wastewater treatment plant (WWTP), for biodegradation of an antidepressant drug, paroxetine, and on a cholesterol-lowering agent, bezafibrate. These compounds were chosen as representatives of extensively used pharmaceuticals. Autochthonous microorganisms from the indicated sources were exposed to the target pharmaceuticals (1 mg/L) in co-metabolism with sodium acetate (500 mg/L) along a two-weeks period, for a total of 7 two-weeks periods (here referred as cycles). Exposures were carried out in batch mode, under different incubation conditions (agitation vs. static). Removal of pharmaceuticals was monitored at the end of each cycle, by analysing the culture medium. For paroxetine, fluoride ion release was also followed as an indicator of defluorination of the molecule. The structure of the bacterial communities was analysed by ARISA (Automated rRNA Intergenic Spacer Analysis), at the beginning of the experiment and at the end of the first and the last cycles to identify substantial changes associated with the time of exposure, the incubation conditions and the presence and type of pharmaceuticals. Incubation conditions affected not only the bacterial community structure, but also the biodegradation efficiency. At the beginning of the experiment, removal of target pharmaceuticals was found to be lower under agitation than under static conditions, but at the end of the experiment, results showed high removal of the pharmaceuticals from the culture medium (>97%) under both conditions, mainly by microbiological processes. For paroxetine, adsorption and abiotic processes also had an important influence on its removal, but defluorination only occurred in the presence of microorganisms. These results highlight that autochthonous microorganisms from estuarine sediments and WWTP sludge have high ability to remove the selected pharmaceuticals with relevant implications for the development of new bioremediation tools for environmental restoration.

Effects of Bacillus aryabhattai TBRC8450 on vibriosis resistance and immune enhancement in Pacific white shrimp, Litopenaeus vannamei

The use of probiotics in aquaculture is a practical alternative to promote animal health and disease prevention. Meanwhile, this practice can also reduce the use of prophylactic antibiotics. The purpose of this study was to identify candidate probiotics that could control pathogen populations in host's gastrointestinal (GI) tract and stimulate host immunity in shrimp aquaculture. Bacillus aryabhattai TBRC8450, a bacterial strain isolated from the environment in a shrimp farm, has an antimicrobial activity against many pathogenic strains of Vibrio harveyi and V. parahaemolyticus. Supplementation of B. aryabhattai to Pacific white shrimp (Litopenaeus vannamei) not only decreased the abundance of Vibrio populations, but also shifted the bacterial community in the shrimp GI tract. We found that supplementation of B. aryabhattai triggered shrimp innate immunity and antioxidant activities. mRNA expression of genes encoding microbial peptides and antioxidant enzymes, including C-type lectin, penaeidin-3, heat shock protein 60, thioredoxin, and ferritin, was significantly upregulated in the hepatopancreas of shrimp fed B. aryabhattai. Furthermore, phenoloxidase activity in the hemocytes and the total antioxidant activity in the plasma were increased, indicating enhanced immune and antioxidant responses at the systemic level. In contrast, supplementation of B. aryabhattai had no effect on the total hemocyte count and superoxide dismutase activity in the plasma and hepatopancreas. Importantly, a pathogen challenge test using V. harveyi 1562 showed a significant increase in survival rates of shrimp fed B. aryabhattai compared to the control group. Our findings suggest that B. aryabhattai TBRC8450 can likely be used as a probiotic to reduce the population of V. harveyi in the shrimp GI tract and to enhance shrimp innate immunity and antioxidant capacity for vibriosis resistance in shrimp aquaculture.

Bacterial density rather than diversity correlates with hatching success across different avian species

Bacterial communities within avian nests are considered an important determinant of egg viability, potentially selecting for traits that confer embryos with protection against trans-shell infection. A high bacterial density on the eggshell increases hatching failure, whether this effect could be due to changes in bacterial community or just a general increase in bacterial density. We explored this idea using intra- and interspecific comparisons of the relationship between hatching success and eggshell bacteria characterized by culture and molecular techniques (fingerprinting and high-throughput sequencing). We collected information for 152 nests belonging to 17 bird species. Hatching failures occurred more frequently in nests with higher density of aerobic mesophilic bacteria on their eggshells. Bacterial community was also related to hatching success, but only when minority bacterial operational taxonomic units were considered. These findings support the hypothesis that bacterial density is a selective agent of embryo viability, and hence a proxy of hatching failure only within species. Although different avian species hold different bacterial densities or assemblages on their eggs, the association between bacteria and hatching success was similar for different species. This result suggests that interspecific differences in antibacterial defenses are responsible for keeping the hatching success at similar levels in different species.