The microbiome impacts host hybridization and speciation

Microbial symbiosis and speciation profoundly shape the composition of life’s biodiversity. Despite the enormous contributions of these two fields to the foundations of modern biology, there is a vast and exciting frontier ahead for research, literature, and conferences to address the neglected prospects of merging their study. Here, we survey and synthesize exemplar cases of how endosymbionts and microbial communities affect animal hybridization and vice versa. We conclude that though the number of case studies remain nascent, the wide-ranging types of animals, microbes, and isolation barriers impacted by hybridization will likely prove general and a major new phase of study that includes the microbiome as part of the functional whole contributing to reproductive isolation. Though microorganisms were proposed to impact animal speciation a century ago, the weight of the evidence supporting this view has now reached a tipping point.

Nitrogen Source Preference and Growth Carbon Costs of Leucaena leucocephala (Lam.) de Wit Saplings in South African Grassland Soils

Leucaena leucocephala (Fabaceae) is native to Central America and has invaded many climatic regions of the tropics. In South Africa, the species is categorized as an emerging or incipient weed used as fodder, timber, firewood and in erosion control on degraded habitats. The species is common along the eastern subtropical regions of KwaZulu-Natal (KZN) Province, where it invades grasslands, savannas and edges of forests. Soils of these ecosystems are characterized as nutrient deficient and acidic. Using a pot trial, we determined the effects of the nutrient addition treatments on microbial symbiosis, N nutrition and biomass accumulation of L. leucocephala under greenhouse conditions. After 180 days of growth, plants were harvested, and their utilization of N derived from the atmosphere and from the soil was quantified through determination of δ15N values. L. leucocephala maintained growth and N nutrition by relying on both atmospheric- and soil-derived N across all soil treatments. The NDFA was significantly higher in high P (N1 + P, N2 + P and N3 + P) soils. L. leucocephala was able to nodulate with intermediate and fast-growing strains from the Mesorhizobium and Rhizobium genus in N2 + P grown plants. This shows that L. leucocephala possesses traits that are successful in acquiring nutrients, especially in nutrient limited conditions, by establishing plant symbiosis with multiple bacteria and relying on extracting N from the soil and from the atmosphere through the symbiosis.

Chromosomal-level genome assembly of the bioluminescent cardinalfish Siphamia tubifer, an emerging model for symbiosis research

The bioluminescent symbiosis between the sea urchin cardinalfish Siphamia tubifer (Kurtiformes: Apogonidae) and the luminous bacterium Photobacterium mandapamensis is an emerging vertebrate-bacteria model for the study of microbial symbiosis. However, there is little genetic data available for the host fish, limiting the scope of potential research that can be carried out with this association. In this study, we present a chromosomal-level genome assembly of S. tubifer using a combination of PacBio HiFi sequencing and Hi-C technologies. The final genome assembly was 1.2 Gb distributed on 23 chromosomes and contained 32,365 protein coding genes with a BUSCO completeness score of 99%. A comparison of the S. tubifer genome to that of another non-luminous cardinalfish revealed a high degree of synteny, whereas a similar comparison to a more distant relative in the Gobiiformes order revealed a fusion of two chromosomes in the cardinalfish genomes. An additional comparison of orthologous clusters among these three genomes revealed a set of 710 clusters that were unique to S. tubifer in which 23 GO pathways were significantly enriched, including several relating to host-microbe interactions and one involved in visceral muscle development, which could be related to the musculature involved in the gut-associated light organ of S. tubifer. We also assembled the complete mitogenome of S. tubifer and discovered both an inversion in the WANCY tRNA gene region resulting in a WACNY gene order as well as heteroplasmy in the length of the control region for this individual. A phylogenetic analysis based on the whole mitochondrial genome indicated that S. tubifer is divergent from the rest of the cardinalfish family, bringing up questions of the involvement of the bioluminescent symbiosis in the initial divergence of the ancestral Siphamia species. This draft genome assembly of S. tubifer will enable future studies investigating the evolution of bioluminescence in fishes as well as candidate genes involved in the symbiosis and will provide novel opportunities to use this system as a vertebrate-bacteria model for symbiosis research.

Gut Bacterial Communities of Lymantria xylina and Their Associations with Host Development and Diet

The gut microbiota of insects has a wide range of effects on host nutrition, physiology, and behavior. The structure of gut microbiota may also be shaped by their environment, causing them to adjust to their hosts; thus, the objective of this study was to examine variations in the morphological traits and gut microbiota of Lymantria xylina in response to natural and artificial diets using high-throughput sequencing. Regarding morphology, the head widths for larvae fed on a sterilized artificial diet were smaller than for larvae fed on a non-sterilized host-plant diet in the early instars. The gut microbiota diversity of L. xylina fed on different diets varied significantly, but did not change during different development periods. This seemed to indicate that vertical inheritance occurred in L. xylina mutualistic symbionts. Acinetobacter and Enterococcus were dominant in/on eggs. In the first instar larvae, Acinetobacter accounted for 33.52% of the sterilized artificial diet treatment, while Enterococcus (67.88%) was the predominant bacteria for the non-sterilized host-plant diet treatment. Gut microbe structures were adapted to both diets through vertical inheritance and self-regulation. This study clarified the impacts of microbial symbiosis on L. xylina and might provide new possibilities for improving the control of these bacteria.

Altering Nitrogen Sources Affects Growth Carbon Costs in Vachellia nilotica Growing in Nutrient-Deficient Grassland Soils

Vachellianilotica (L.) Willd. Ex Del. is a multipurpose leguminous tree that is common in grassland and savanna ecosystems in southern and eastern Africa. These ecosystem soils are reported to be acidic and nutrient-limited, specifically with regards to nitrogen (N) and phosphorus (P). The presence of this plant in these terrestrial ecosystems improves soil fertility benefiting the surrounding vegetation due to its ability to fix atmospheric N. This study seeks to understand the N-fixing bacteria symbiosis and physiological adaptations of V. nilotica in these acidic and nutrient-deficient KwaZulu-Natal soils. The soils used for this study were collected from the Ukulinga Grassland Nutrient Experiment located at the Ukulinga research farm of the University of KwaZulu-Natal, Pietermaritzburg, South Africa. Due to long-term soil nutrient addition treatments, these soils offered a diverse nutrient variation for better understanding the effects of acidity and nutrient variation on microbial symbiosis, plant nutrition, and biomass accumulation of V. nilotica. V. nilotica was able to maintain growth by relying on both atmospheric and soil-derived N across all treatments decreasing carbon (C) growth costs. There was an increased reliance on atmospheric-derived N of un-nodulated high N-treated plants. The plants grown in high N + P soils were able to nodulate with various species from the Mesorhizobium genus, which resulted in increased biomass compared to other plants. The results of this study show that V. nilotica can alter N sources to reduce C growth costs. In addition, both nodulating and free-living soil N2 fixing bacteria such as Caulobacter rhizosphaerae, Sphingomonas sp. and Burkholderia contaminans identified in the experimental soils may play an important role under P-deficient conditions.

Covid and Oxytocin: Looking for Microbial Symbiosis

Oxytocin is a hormone with broad implications for general health. This hormone has anti-inflammatory and antioxidant protective effects and has received particular attention due to the pandemic of COVID-19. This review examines materials on the role of microbial symbiosis in COVID-19 and the effect of microbiota on oxytocin. It opens new potential prospects for the use of microbiota and new “nature-like” technologies.

Altering Nitrogen Sources Affects Growth Carbon Costs in Vachellia nilotica Growing in Nutrient Deficient Grassland Soils

Vachellia nilotica (L.) Willd. Ex Del. is multipurpose leguminous tree which is common in grass-land and savanna ecosystems in southern and eastern Africa. These ecosystem soils are reported to be acidic and nutrient limited, specifically with regards to nitrogen (N) and phosphorus (P). The presence of this plant in these terrestrial ecosystems improves soil fertility benefiting the sur-rounding vegetation due to its ability fix atmospheric N. This study seeks to understand the mi-crobial symbiosis and physiological adaptations of V. nilotica in these acidic and nutrient defi-cient KZN soils. The soils used for this study were collected from the Ukulinga Grassland Nutri-ent Experiment located at the Ukulinga research farm of the University of KwaZulu-Natal, Pie-termaritzburg, South Africa. Due to long-term soil nutrient addition treatments, these soils of-fered a diverse nutrient variation for better understanding the effects of acidity and nutrient var-iation on microbial symbiosis, plant nutrition and biomass accumulation of V. nilotica. V. nilotica was able to maintain growth by relying on both atmospheric and soil derived N across all treat-ments decreasing carbon (C) growth costs. There was an increased reliance on atmospheric de-rived N of un-nodulated high N treated plants. The plants grown in high N+P soils were able to nodulate with various species from the Mesorhizobium genus which resulted in an increased bio-mass compared to other plants. The results of this study show that V. nilotica can alter N sources to reduce C growth costs. Also, free-living N2 fixing bacteria play an important role under P deficient conditions.

The Keystone commensal bacterium Christensenella minuta DSM 22607 displays anti-inflammatory properties both in vitro and in vivo

Christensenellaceae is a family of subdominant commensal bacteria found in humans. It is thought to play an important role in gut health by maintaining microbial symbiosis. Indeed, these bacteria occur at significantly lower levels or are absent in individuals suffering from inflammatory bowel diseases (IBDs). Here, we explored if type species Christensenella minuta (strain: DSM 22607) could have the potential to help treat IBDs. We assessed key properties displayed by the bacterium using a combination of in vitro and in vivo assays. We found that while C. minuta is a strict anaerobe, it is also oxygen tolerant. Additionally, we observed that the species produces high levels of acetate and moderate levels of butyrate. We performed deep phenotyping using Biolog microarrays. Using human intestinal cell lines, we discovered that C. minuta demonstrated strong anti-inflammatory activity, resulting in reduced levels of proinflammatory IL-8 cytokines via the inhibition of the NF-κB signaling pathway. Furthermore, C. minuta protected intestinal epithelial integrity in vitro. Finally, in two distinct animal models of acute colitis, C. minuta prevented intestinal damage, reduced colonic inflammation, and promoted mucosal healing. Together, these results indicate that C. minuta has potent immunomodulatory properties, underscoring its potential use in innovative microbiome-based IBD biotherapies.