Beekeepers struggle to minimize the mortality of their colonies as a consequence of the parasitic mite Varroa destructor in order to maintain a sustainable managed pollinator population. However, little is known about how varroa mites might diminish local populations of honey bee males (drones) that might affect the mating success of queens. As one of the world’s last localities invaded by varroa mites, the Hawaiian Islands offer a unique opportunity to examine this question by comparing queens mated on mite-infested and mite-free islands. We raised queen bees on four Hawaiian Islands (Kaua‘i, O‘ahu, Maui, and Hawai‘i) and subsequently collected their offspring to determine queen mating frequency and insemination success. No significant difference for mating success was found between the islands with and without varroa mites, and relatively high levels of polyandry was detected overall. We also found a significant association between the number of sperm stored in the queens’ spermathecae and the number of managed colonies within the localities of the queens mated. Our findings suggest that varroa mites, as they currently occur in Hawai‘i, may not significantly reduce mating success of honey bee queens, which provides insight for both the reproductive biology of honey bees as well as the apiculture industry in Hawai‘i.

Typical bacterial GH30 xylanases are glucuronoxylanases requiring 4-O-methylglucuronic acid (MeGlcA) substitution of a xylan main chain for their action. They do not exhibit a significant activity on neutral xylooligosaccharides, arabinoxylan (AraX), or rhodymenan (Rho). In this work, the biochemical characterization of the bacterial Clocl_1795 xylanase from Hungateiclostridium (Clostridium) clariflavum DSM 19732 (HcXyn30A) is presented. Amino acid sequence analysis of HcXyn30A revealed that the enzyme does not contain amino acids known to be responsible for MeGlcA coordination in the -2b subsite of glucuronoxylanases. This suggested that the catalytic properties of HcXyn30A may differ from those of glucuronoxylanases. HcXyn30A shows similar specific activity on glucuronoxylan (GX) and Rho, while the specific activity on AraX is about 1000 times lower. HcXyn30A releases Xyl₂ as the main product from the non-reducing end of different polymeric and oligomeric substrates. Catalytic properties of HcXyn30A resemble the properties of the fungal GH30 xylobiohydrolase from Acremonium alcalophilum, AaXyn30A. HcXyn30A is the first representative of a prokaryotic xylobiohydrolase. Its unique specificity broadens the catalytic diversity of bacterial GH30 xylanases.

Key points

• Bacterial GH30 xylobiohydrolase from H. clariflavum (HcXyn30A) has been characterized.

• HcXyn30A releases xylobiose from the non-reducing end of different substrates.

• HcXyn30A is the first representative of bacterial xylobiohydrolase.

Recent advances in sequencing technologies have shown that there are a few hundred species of microorganisms associated with plants both below and above ground, with the roots being a major staging ground for the strongest functional interactions. Plants interact closely with their endophytes and with microorganisms growing on the root surface and in the rhizosphere. This plant microbiome constitutes a complementary genome in service of the plant and there is growing evidence that it can be manipulated to benefit plant growth and productivity. The most effective form of manipulation has been to use beneficial microorganisms, either singly or in combination to improve the yield by what is generally termed growth promotion or as biocontrol agents that eliminate or reduce the deleterious effects of pathogens. Until recently the ability to study the influence of the added inoculant on the other microorganisms was limited to a few members of cultured species whereas after the explosive development of sequencing technologies and bioinformatic tools there can be a more comprehensive coverage of the effects on the microbiome. This chapter discusses these developments and the emergence of analytical tools to study networks of members of microbiomes as well as mechanisms to manipulate and engineer microbiomes.

The microbial H₂-producing (hydrogenogenic) carbon monoxide (CO)-oxidizing activity by the membrane-associated CO dehydrogenase (CODH)/energy-converting hydrogenase (ECH) complex is an important metabolic process in the microbial community. However, the studies on hydrogenogenic carboxydotrophs had to rely on inherently cultivation and isolation methods due to their rare abundance, which was a bottleneck in ecological study. Here, we provided gene-targeted sequencing method for the diversity estimation of thermophilic hydrogenogenic carboxydotrophs. We designed six new degenerate primer pairs which effectively amplified the coding regions of CODH genes forming gene clusters with ECH genes (CODHech genes) in Firmicutes which includes major thermophilic hydrogenogenic carboxydotrophs in terrestrial thermal habitats. Amplicon sequencing by these primers using DNAs from terrestrial hydrothermal sediments and CO-gas-incubated samples specifically detected multiple CODH genes which were identical or phylogenetically related to the CODHech genes in Firmictes. Furthermore, we found that phylogenetically distinct CODHech genes were enriched in CO-gas-incubated samples, suggesting that our primers detected uncultured hydrogenogenic carboxydotrophs as well. The new CODH-targeted primers provided us with a fine-grained (~ 97.9% in nucleotide sequence identity) diversity analysis of thermophilic hydrogenogenic carboxydotrophs by amplicon sequencing and will bolster the ecological study of these microorganisms.

The honeybee Apis mellifera L. is a crucial pollinator as well as a prominent scientific model organism, in particular for the neurobiological study of olfactory perception, learning, and memory. A wealth of information is indeed available about how the worker bee brain detects, processes, and learns about odorants. Comparatively, olfaction in males (the drones) and queens has received less attention, although they engage in a fascinating mating behavior that strongly relies on olfaction. Here, we present our current understanding of the molecules, cells, and circuits underlying bees’ sexual communication. Mating in honeybees takes place at so-called drone congregation areas and places high in the air where thousands of drones gather and mate in dozens with virgin queens. One major queen-produced olfactory signal—9-ODA, the major component of the queen pheromone—has been known for decades to attract the drones. Since then, some of the neural pathways responsible for the processing of this pheromone have been unraveled. However, olfactory receptor expression as well as brain neuroanatomical data point to the existence of three additional major pathways in the drone brain, hinting at the existence of 4 major odorant cues involved in honeybee mating. We discuss current evidence about additional not only queen- but also drone-produced pheromonal signals possibly involved in bees’ sexual behavior. We also examine data revealing recent evolutionary changes in drone’s olfactory system in the Apis genus. Lastly, we present promising research avenues for progressing in our understanding of the neural basis of bees mating behavior.

In an aquifer-aquitard system in the subsoil of the city of Ferrara (Emilia-Romagna region, northern Italy) highly contaminated with chlorinated aliphatic toxic organics such as trichloroethylene (TCE) and tetrachloroethylene (PCE), a strong microbial-dependent dechlorination activity takes place during migration of contaminants through shallow organic-rich layers with peat intercalations. The in situ microbial degradation of chlorinated ethenes, formerly inferred by the utilization of contaminant concentration profiles and Compound-Specific Isotope Analysis (CSIA), was here assessed using Illumina sequencing of V4 hypervariable region of 16S rRNA gene and by clone library analysis of dehalogenase metabolic genes. Taxon-specific investigation of the microbial communities catalyzing the chlorination process revealed the presence of not only dehalogenating genera such as Dehalococcoides and Dehalobacter but also of numerous other groups of non-dehalogenating bacteria and archaea thriving on diverse metabolisms such as hydrolysis and fermentation of complex organic matter, acidogenesis, acetogenesis, and methanogenesis, which can indirectly support the reductive dechlorination process. Besides, the diversity of genes encoding some reductive dehalogenases was also analyzed. Geochemical and 16S rRNA and RDH gene analyses, as a whole, provided insights into the microbial community complexity and the distribution of potential dechlorinators. Based on the data obtained, a possible network of metabolic interactions has been hypothesized to obtain an effective reductive dechlorination process.

Aims

Phytoremediation of soil contaminated by trace elements is a technology using plants and microorganisms to sequester, inactivate, or extract contaminants from the soil. The assemblage formed by the partnership between plants and microorganisms is referred to as the plant holobiont concept. Among holobiont microorganisms, endophytes are associated with the plant at its earliest growth stage and are localized inside plant tissues. While plant tissues shelter endophytic microbial communities, mutualistic endophytes have shown a potential for plant growth promotion that will deeply and durably benefit the plant holobiont. In this review, we describe the state-of-the-art knowledge of the endophytes’ role in plant growth promotion and the prospects for phytoremediation technologies.

Results

Mutualistic symbionts have been demonstrated to improve plant growth, germination and yield. Indeed, they improve plant nutrition, increase plant resistance to bio-aggressors and stimulate plant metabolite productions. Research has shown that endophytes improve plant performance especially under extreme conditions such as drought, nitrogen deficiency, salinity and exposition to metal phytotoxicity. Endophyte inoculation has shown potential for plant growth promotion and has increased metal translocation in hyperaccumulator shoots by mitigating stresses from contaminated and naturally metal-rich soils.

Conclusions

Endophytes have demonstrated their potential to enhance the plant’s physiological status under metallic stress, the growth of both roots and shoots, as well as increasing metal uptake in the shoot biomass of a wide diversity of hyperaccumulating plants. Endophyte-assisted phytoremediation is a promising technology for the remediation of polluted or naturally metal-rich soils.

Microorganisms isolated from various traditionally fermented food products prepared in households without commercial starter cultures are designated as natural isolates. In addition, this term is also used for microorganisms collected from various natural habitats or products (silage, soil, manure, plant and animal material, etc.) that do not contain any commercial starters or bacterial formulations. They are characterized by unique traits that are the result of the selective pressure of environmental conditions, as well as interactions with other organisms. The synthesis of antimicrobial molecules, including bacteriocins, is an evolutionary advantage and an adaptive feature that sets them apart from other microorganisms from a common environment. This review aims to underline the knowledge of bacteriocins produced by natural isolates, with a particular emphasis on the most common location of their genes and operons, plasmids, and the importance of the relationship between the plasmidome and the adaptive potential of the isolate. Applications of bacteriocins, ranging from natural food preservatives to supplements and drugs in pharmacology and medicine, will also be addressed. The latest challenges faced by researchers in isolating new natural isolates with desired characteristics will be discussed, as well as the production of new antimicrobials, nearly one century since the first discovery of colicins in 1925.

Key points

• Natural bacterial isolates harbor unique properties shaped by diverse interactions.

• Horizontal gene transfer enables constant engineering of new antimicrobials.

• Fermented food products are important source of bacteriocin-producing natural isolates.

The genus Rhizobium is well known in the context of its interaction with leguminous plants. The symbiosis Rhizobium-legume constitutes a significant source of ammonia in the biosphere. Rhizobium species have been studied and applied as biofertilizers for decades in legumes and nonlegumes, due to the potential as N-fixer and plant growth promoter. Since its discovery, conventional culture-dependent techniques were used to isolate Rhizobium members from their natural niche, the nodule, and their identification was routinely performed via 16S rRNA gene and different housekeeping genes. Biotechnological advances based on the use of omics-based technologies showed that species belonging to the genus Rhizobium are keystone taxa in several diverse environments, such as forests, agricultural land, Arctic, and Antarctic ecosystems, contaminated soils and plant-associated microbiota. In this chapter, we will summarize the advances in the study of the Rhizobium genus, from culturomics strategies to modern omics methodologies, mostly based on next-generation sequencing approaches. These cutting-edge molecular approaches are fundamental in the study of the behavior of Rhizobium species in their interaction with Non-leguminous plants, supporting their potential as an ecological alternative to chemical fertilizers in the battle against Climatic Change.

Extremophiles are microorganisms that flourish in habitats of extreme environments, including in high concentration of salts, pollutants, high or low temperature, an acidic or alkaline pH. All extreme environments are dominated by microorganisms belonging to Archaea, the third domain of life, evolutionary distinct from Bacteria and Eucarya. Over the past few years, the molecular biology of extremophilic Archaea has stimulated a lot of interest in the field of bioremediation. Bioremediation is the use of microorganisms for the degradation or removal of contaminants. Contamination of soils, sediments and water due to anthropogenic activities is a matter of concern at global level. Bioremediation has emerged as an effective solution for these problems. Most bioremediation research has focused on the processes performed by the domain Bacteria. Recently, extremophiles are the focus of growing interest for bioremediation because they can tolerate very harsh environmental conditions due to their ability to produce an array of molecules or extremozymes capable of functioning in the environment without denaturing. These extremozymes from extremophilic microorganisms have special characteristics such as stability to elevated temperature, extremes of pH, organic solvents and high ion strength. Due to the stability and persistence of these extremophilic microorganisms under adverse environmental conditions, they can be explored finding new species for using in the bioremediation of environments contaminated with extremely recalcitrant pollutants. Here, we provide an overview of the archaeal extremophilic microorganisms such as thermopiles, acidophiles, halophiles which have potential applications in the field of bioremediation of environmental pollutants, including hydrocarbons, heavy metals, pesticides, petroleum and wastewater treatments.