Characterization of Bifidobacterium apousia sp. nov., Bifidobacterium choladohabitans sp. nov., and Bifidobacterium polysaccharolyticum sp. nov., three novel species of the genus Bifidobacterium from honey bee gut

Bifidobacterium is one of the dominating bacterial genera in the honey bee gut, and they are the key degrader of diet polysaccharides for the host. Previous genomic analysis shows that they belong to separate phylogenetic clusters and exhibited different functional potentials in hemicellulose digestion. Here, three novel strains from the genus Bifidobacterium were isolated from the guts of the honey bee (Apis mellifera). Phylogenomic analysis showed that the isolates could be grouped into four phylogenetic clusters. The average nucleotide identity values between strains from different clusters are <95%, while strains in Cluster IV belong to the characterized species Bifidobacterium asteroides. Carbohydrate-active enzyme annotation confirmed that the metabolic capacity for carbohydrates varied between clusters of strains. Cells are Gram-positive rods; they grew both anaerobically and in a CO₂-enriched atmosphere. All strains grew at a temperature range of 20–42 °C, with optimum growth at 35 °C. The pH range for growth was 5–9. Strains from different phylogenetic clusters varied in multiple phenotypic and chemotaxonomic characterizations. Thus, we propose three novel species Bifidobacterium apousia sp. nov. whose type strain is W8102^T (=CGMCC 1.18893 ^T = JCM 34587 ^T), Bifidobacterium choladohabitans sp. nov., whose type strain is B14384H11^T (=CGMCC 1.18892 ^T = JCM 34586 ^T), and Bifidobacterium polysaccharolyticum sp. nov. whose type strain is W8117^T (=CGMCC 1.18894 ^T = JCM 34588 ^T).     

Contribution of peeling host for epiphyte abundance in two tropical dry forests in the “El Cielo Biosphere Reserve”, Mexico

Host traits partly determine the abundance and species richness of epiphytes in tropical forests. It has been proposed that older trees with rough bark and evergreens often house more individuals and more epiphytic species than those with thin, smooth, and peeling bark, which harbor few epiphytes. We hypothesize (i) that epiphytes are more abundant and species-rich in the more shaded forest, which is related to bark roughness, and (ii) that epiphytes are distributed in the middle of the host, where microenvironmental conditions are more favorable to survival. We evaluated abundance, species richness, and vertical distribution of epiphytes in two tropical dry forests, according to the deciduousness and basal area of the trees. Moreover, we selected the most abundant epiphytes to test whether their distribution is related to a specific bark type and examine their vertical distribution in two dry forests. We distinguished a high abundance and species richness of epiphytes in the deciduous forest, although basal area and host species richness were higher in the semi-deciduous forest. In both forests, we found a positive relationship between epiphyte abundance and basal area. Higher abundance of epiphytes was related to the predominance of Tillandsia schiedeana, a drought-adapted species, in both forests. Unexpectedly, epiphytes abundantly colonized Bursera simaruba, a host with peeling bark and a very branched crown, where small individuals of T. schiedeana colonized abundantly toward the top of the crown. Our results show the importance of the tropical dry forest, particularly, B. simaruba, in maintaining epiphyte diversity in terms of T. schiedeana colonization.     

Inconsistent detection of extinction debts using different methods

The extinction debt, delayed species extinctions following landscape degradation, is a widely discussed concept. But a consensus about the prevalence of extinctions debts is hindered by a multiplicity of methods and a lack of comparisons among habitats. We applied three contrasting species–area relationship methods to test for plant community extinction debts in three habitats which had different degradation histories over the last century: calcareous grassland, heathland and woodland. These methods differ in their data requirements, with the first two using information on past and current habitat area alongside current species richness, whilst the last method also requires data on past species richness. The most data‐intensive, and hence arguably most reliable method, identified extinction debts across all habitats for specialist species, whilst the other methods did not. All methods detected an extinction debt in calcareous grassland, which had undergone the most severe degradation. We conclude that some methods failed to detect an extinction debt, particularly in habitats that have undergone moderate degradation. Data on past species numbers are required for the most reliable method; as such data are rare, extinction debts may be under‐reported.     

Morphology and molecular phylogeny of the anaerobic freshwater ciliate Urostomides spinosus nov. spec. (Ciliophora,Armophorea, Metopida) from China

The morphology and molecular phylogeny of a new metopid ciliate, Urostomides spinosus nov. spec., discovered in a freshwater ditch in Qingdao, China, were investigated using live observation, morphometry and protargol staining as well as molecular phylogenetic methods. Diagnostic features of the new species include a broadly obpyriform body carrying three posterior spines, eight somatic kineties, five preoral dome kineties with specialized row 3, adoral zone composed of about 28 membranelles, making a 270° turn around body axis. Phylogenetic analyses of the SSU rDNA sequence revealed that the genus Urostomides is monophyletic, but its interspecific relationships remained unresolved. Moreover, a closer relationship of the new species with the morphologically similar Urostomides campanula was not supported by the molecular data.     

Competitive strategies between Anastrepha fraterculus and Anastrepha obliqua (Diptera: Tephritidae) regulating the use of host fruits

Interspecific competition between individuals of different species can result in reductions in their fecundity, growth or survival, reflecting differential exploitation of resources that become intensified due to spatial co-occurrence, ecological similarity and increased population densities. As two species cannot occupy the same niche, coexistence is only possible if the available resources are used in non-overlapping manners such as niche partitioning or the use of refuges. Among agricultural insect pests, such as fruit flies of the family Tephritidae, competitive interactions can result in competitive displacement, host changes, or the expansion or restriction of the numbers of hosts utilized that can have negative consequences for human agricultural activities. We evaluated the competitive interactions between two fruit fly species of the genus Anastrepha, Anastrepha obliqua (Macquart, 1835) and Anastrepha fraterculus (Wiedmann, 1830), on their respective preferred hosts (mangoes and guava). Experiments of larval competition and competition for ovipositioning sites by adult females were performed to compare the parameters of larval development time, numbers of pupae and emerged adults and numbers of ovipositions in the presence or absence of interspecific competition. We observed that the interactions between those species were asymmetrical and hierarchical, and our results suggest a competitive displacement of A. fraterculus by A. obliqua when those two species are present on the same fruit, whether mangoes or guavas.     

An efficient Oligo-FISH painting system for revealing chromosome rearrangements and polyploidization in Triticeae

A chromosome-specific painting technique has been developed which combines the most recent approaches of the companion disciplines of molecular cytogenetics and genome research. We developed seven oligonucleotide (oligo) pools derivd from single-copy sequences on chromosomes 1 to 7 of barley (Hordeum vulgare L.) and corresponding collinear regions of wheat (Triticum aestivum L.). The seven groups of pooled oligos comprised between 10 986 and 12 496 45-bp monomers, and these then produced stable fluorescence in situ hybridization (FISH) signals on chromosomes of each linkage group of wheat and barley. The pooled oligo probes were applied to high-throughput karyotyping of the chromosomes of other Triticeae species in the genera Secale, Aegilops, Thinopyrum, and Dasypyrum, and the study also extended to some wheat-alien amphiploids and derived lines. We demonstrated that a complete set of whole-chromosome oligo painting probes facilitated the study of inter-species chromosome homologous relationships and visualized non-homologous chromosomal rearrangements in Triticeae species and some wheat-alien species derivatives. When combined with other non-denaturing FISH procedures using tandem-repeat oligos, the newly developed oligo painting techniques provide an efficient tool for the study of chromosome structure, organization, and evolution among any wild Triticeae species with non-sequenced genomes.     

A Plasmopara viticola RXLR effector targets a chloroplast protein PsbP to inhibit ROS production in grapevine

Pathogens secrete a large number of effectors that manipulate host processes to create an environment conducive to pathogen colonization. However, the underlying mechanisms by which Plasmopara viticola effectors manipulate host plant cells remain largely unclear. In this study, we reported that RXLR31154, a P. viticola RXLR effector, was highly expressed during the early stages of P. viticola infection. In our study, stable expression of RXLR31154 in grapevine (Vitis vinifera) and Nicotiana benthamiana promoted leaf colonization by P. viticola and Phytophthora capsici, respectively. By yeast two-hybrid screening, the 23-kDa oxygen-evolving enhancer 2 (VpOEE2 or VpPsbP), encoded by the PsbP gene, in Vitis piasezkii accession Liuba-8 was identified as a host target of RXLR31154. Overexpression of VpPsbP enhanced susceptibility to P. viticola in grapevine and P. capsici in N. benthamiana, and silencing of NbPsbPs, the homologs of PsbP in N. benthamiana, reduced P. capcisi colonization, indicating that PsbP is a susceptibility factor. RXLR31154 and VpPsbP protein were co-localized in the chloroplast. Moreover, VpPsbP reduced H₂O₂ accumulation and activated the ¹O₂ signaling pathway in grapevine. RXLR31154 could stabilize PsbP. Together, our data revealed that RXLR31154 reduces H₂O₂ accumulation and activates the ¹O₂ signaling pathway through stabilizing PsbP, thereby promoting disease.     

Pre treatment with Bacillus subtilis mitigates drought induced photo-oxidative damages in okra by modulating antioxidant system and photochemical activity

Growth promoting potential of Bacillus subtilis (BS) in drought stressed Abelmoschus esculentus (L.) Moench (okra) was assessed by measuring the chlorophyll stability index (CSI), chlorophyll a (Chl-a) fluorescence, leaf osmotic potential and lipid peroxidation by malondialdehyde content, emission of reactive oxygen species (ROS), osmolyte content and the activity of non-enzyme and enzyme antioxidants. BS treatment significantly increased the leaf osmotic potential, osmolyte production and the activity of non-enzyme and enzyme antioxidants under drought stress. BS treatment mitigated the drought-induced reduction in Chl a fluorescence and CSI. Concomitant increase in total sugar, proline, non-enzyme antioxidants [glutathione and ascorbate] and enzyme antioxidants like superoxide dismutase, catalase, ascorbate peroxidase, glutathione reductase, monodehydroascorbate reductase and dehydroascorbate reductase modulate the intracellular ROS concentration in okra to resist the stress induced oxidative damage in BS treated plants led to fast recovery and less photodamage.Supplementary InformationThe online version contains supplementary material available at 10.1007/s12298-021-00982-8.     

Relationship between aquifer biofilms and unattached microbial indicators of urban groundwater contamination

Aquifers, springs and other groundwater‐dependent ecosystems are threatened by urban land use, which causes water quality deterioration through nutrient loading, sewage infiltration, groundwater extraction and, along coasts, seawater intrusion. The presence of certain microbes in groundwater can indicate that an aquifer is anthropogenically contaminated. Interpretations made from observations of indicator microbes in groundwater are limited because the relationship between the presumably allochthonous indicator microbes and relevant autochthonous microbial communities has not been characterized. This study addressed whether autochthonous aquifer biofilms can influence the presence of presumed microbial indicators in groundwater, and simultaneously used microbial indicators to trace sources of urban contamination at a karst spring of conservation concern. These questions were approached using a 17‐month time series analysis of attached biofilm and adjacent unattached bacteria in the submerged karst aquifer conduit associated with this spring. Environmental 16S rRNA gene sequencing was performed to characterize these communities, and community structure data were contextualized with groundwater geochemical and hydrogeological measurements. Linear regression models were developed to explain the relative abundance patterns of indicator microbes and other unattached microbes at this site. The results of this study suggest that dominant aquifer biofilms do not influence the presence of unattached microbial taxa that are presumed to be indicators of groundwater contamination, and generated new information about the origin of coliform bacteria at the study site. These results build confidence in the use of microbial indicators in groundwater‐dependent ecosystem conservation strategies and inform future management plans for urban aquifers and springs worldwide.