scholarly journals Opportunities and Challenges to Microbial Symbiosis Research in the Microbiome Era

2020 ◽  
Vol 11 ◽  
Author(s):  
Suhelen Egan ◽  
Takema Fukatsu ◽  
M. Pilar Francino
Keyword(s):  
Microbial Symbiosis ◽  
Symbiosis Research

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

2021 ◽  
Author(s):  
Alison L Gould ◽  
James B Henderson ◽  
Athena W Lam
Keyword(s):  
Genome Assembly ◽  
Muscle Development ◽  
Draft Genome ◽  
Protein Coding ◽  
Draft Genome Assembly ◽  
Microbe Interactions ◽  
Host Microbe Interactions ◽  
Microbial Symbiosis ◽  
Symbiosis Research ◽  
Siphamia Tubifer

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.

scholarly journals Dramatic differences in gut bacterial densities help to explain the relationship between diet and habitat in rainforest ants

2017 ◽  
Author(s):  
Jon G Sanders ◽  
Piotr Lukasik ◽  
Megan E Frederickson ◽  
Jacob A Russell ◽  
Ryuichi Koga ◽  
...  
Keyword(s):  
16S Rrna ◽  
Microbial Diversity ◽  
Tropical Rainforest ◽  
Amplicon Sequencing ◽  
Sequencing Data ◽  
Lowland Tropical Forest ◽  
16S Rrna Amplicon Sequencing ◽  
Microbial Symbionts ◽  
Microbial Symbiosis ◽  
Diversity Profiles

AbstractAbundance is a key parameter in microbial ecology, and important to estimates of potential metabolite flux, impacts of dispersal, and sensitivity of samples to technical biases such as laboratory contamination. However, modern amplicon-based sequencing techniques by themselves typically provide no information about the absolute abundance of microbes. Here, we use fluorescence microscopy and quantitative PCR as independent estimates of microbial abundance to test the hypothesis that microbial symbionts have enabled ants to dominate tropical rainforest canopies by facilitating herbivorous diets, and compare these methods to microbial diversity profiles from 16S rRNA amplicon sequencing. Through a systematic survey of ants from a lowland tropical forest, we show that the density of gut microbiota varies across several orders of magnitude among ant lineages, with median individuals from many genera only marginally above detection limits. Supporting the hypothesis that microbial symbiosis is important to dominance in the canopy, we find that the abundance of gut bacteria is positively correlated with stable isotope proxies of herbivory among canopy-dwelling ants, but not among ground-dwelling ants. Notably, these broad findings are much more evident in the quantitative data than in the 16S rRNA sequencing data. Our results help to resolve a longstanding question in tropical rainforest ecology, and have broad implications for the interpretation of sequence-based surveys of microbial diversity.

scholarly journals Exaiptasia diaphana from the great barrier reef: a valuable resource for coral symbiosis research

Symbiosis ◽  
2020 ◽  
Vol 80 (2) ◽  
pp. 195-206 ◽  
Author(s):  
Ashley M. Dungan ◽  
Leon M. Hartman ◽  
Giada Tortorelli ◽  
Roy Belderok ◽  
Annika M. Lamb ◽  
...  
Keyword(s):  
Great Barrier Reef ◽  
Barrier Reef ◽  
Valuable Resource ◽  
Symbiosis Research

A Century of Synergy in Termite Symbiosis Research: Linking the Past with New Genomic Insights

2021 ◽  
Vol 66 (1) ◽  
pp. 23-43
Author(s):  
Michael E. Scharf ◽  
Brittany F. Peterson
Keyword(s):  
Nineteenth Century ◽  
Twentieth Century ◽  
Late Nineteenth Century ◽  
Symbiotic Associations ◽  
The Past ◽  
Gas Utilization ◽  
Biochemical Studies ◽  
Late Nineteenth ◽  
Symbiosis Research ◽  
Culture Dependent

Termites have long been studied for their symbiotic associations with gut microbes. In the late nineteenth century, this relationship was poorly understood and captured the interest of parasitologists such as Joseph Leidy; this research led to that of twentieth-century biologists and entomologists including Cleveland, Hungate, Trager, and Lüscher. Early insights came via microscopy, organismal, and defaunation studies, which led to descriptions of microbes present, descriptions of the roles of symbionts in lignocellulose digestion, and early insights into energy gas utilization by the host termite. Focus then progressed to culture-dependent microbiology and biochemical studies of host–symbiont complementarity, which revealed specific microhabitat requirements for symbionts and noncellulosic mechanisms of symbiosis (e.g., N2 fixation). Today, knowledge on termite symbiosis has accrued exponentially thanks to omic technologies that reveal symbiont identities, functions, and interdependence, as well as intricacies of host–symbiont complementarity. Moving forward, the merging of classical twentieth-century approaches with evolving omic tools should provide even deeper insights into host–symbiont interplay.

Natural Polymorphisms in a Pair of NSP2 Homoeologs Can Cause Loss of Nodulation in Peanut

2020 ◽  
Author(s):  
Ze Peng ◽  
Huiqiong Chen ◽  
Lubin Tan ◽  
Hongmei Shu ◽  
Rajeev K Varshney ◽  
...  
Keyword(s):  
Genetic Basis ◽  
Molecular Mechanisms ◽  
Root Nodules ◽  
Germplasm Collection ◽  
Mendelian Inheritance ◽  
Legume Crop ◽  
Arachis Hypogaea L ◽  
Transcription Factor Genes ◽  
Cultivated Peanut ◽  
Microbial Symbiosis

Abstract Microbial symbiosis in legumes is achieved through nitrogen-fixing root nodules, which is important for sustainable agriculture. The molecular mechanisms underlying development of root nodules in polyploid legume crops are largely understudied. Through map-based cloning and QTL-seq approaches, we identified a pair of homoeologous GRAS transcription factor genes, Nodulation Signaling Pathway 2 (AhNSP2-B07 or Nb) and AhNSP2-A08 (Na), controlling nodulation in cultivated peanut (Arachis hypogaea L.), an allotetraploid legume crop, which exhibited non-Mendelian and Mendelian inheritance, respectively. The segregation of nodulation in the progeny of Nananbnb genotypes followed a 3:1 Mendelian ratio, in contrast to the 5:3 ~ 1:1 non-Mendelian ratio for nanaNbnb genotypes. Additionally, a much higher frequency of the nb allele (13%) than the na allele (4%) exists in the peanut germplasm collection, suggesting that Nb is less essential than Na in nodule organogenesis. Our findings provided the genetic basis of naturally occurred non-nodulating peanut plants, which can be potentially used for nitrogen fixation improvement in peanut. Furthermore, the results provided implications and insights into the evolution of homoeologous genes in allopolyploid species.

scholarly journals Microbial symbiosis and coevolution of an entire clade of ancient vertebrates: the gut microbiota of sea turtles and its relationship to their phylogenetic history

2020 ◽  
Vol 2 (1) ◽  
Author(s):  
Titus Franciscus Scheelings ◽  
Robert J. Moore ◽  
Thi Thu Hao Van ◽  
Marcel Klaassen ◽  
Richard D. Reina
Keyword(s):  
Gut Microbiota ◽  
Sea Turtles ◽  
Microbial Symbiosis

scholarly journals Tryptophan as a Central Hub for Host/Microbial Symbiosis

2020 ◽  
Vol 13 ◽  
pp. 117864692091975 ◽  
Author(s):  
Monica Borghi ◽  
Matteo Puccetti ◽  
Marilena Pariano ◽  
Giorgia Renga ◽  
Claudia Stincardini ◽  
...  
Keyword(s):  
Immune System ◽  
Amino Acid ◽  
Fungal Infections ◽  
Antibiotic Use ◽  
Commensal Bacteria ◽  
Mammalian Host ◽  
Amino Acid Catabolism ◽  
Opportunistic Fungi ◽  
Microbial Symbiosis

Amino acid catabolism occurs during inflammation and regulates innate and adaptive immunity. The role of commensal bacteria in amino acid catabolism and the production of metabolites able to regulate the development and function of the innate immune system is increasingly being recognized. Therefore, commensal bacteria are key players in the maintenance of immune homeostasis. However, the intestinal microbiota also contributes to susceptibility and response to infectious diseases. This is self-evident for fungal infections known to occur as a consequence of weakened immune system and broad-spectrum antibiotic use or abuse. Thus, diseases caused by opportunistic fungi can no longer be viewed as dependent only on a weakened host but also on a disrupted microbiota. Based on these premises, the present review focuses on the role of amino acid metabolic pathways in the dialogue between the mammalian host and its microbiota and the potential implications in fungal commensalism and infectivity.

scholarly journals A Rice Gene for Microbial Symbiosis,Oryza sativaCCaMK, Reduces CH4Flux in a Paddy Field with Low Nitrogen Input

2014 ◽  
Vol 80 (6) ◽  
pp. 1995-2003 ◽  
Author(s):  
Zhihua Bao ◽  
Aya Watanabe ◽  
Kazuhiro Sasaki ◽  
Takashi Okubo ◽  
Takeshi Tokida ◽  
...  
Keyword(s):  
Copy Number ◽  
Root Zone ◽  
Central Component ◽  
Symbiotic Relationships ◽  
Dependent Protein ◽  
The Common ◽  
Microbial Symbiosis ◽  
Methyl Coenzyme M Reductase ◽  
Low Nitrogen

ABSTRACTPlants have mutualistic symbiotic relationships with rhizobia and fungi by the common symbiosis pathway, of which Ca2+/calmodulin-dependent protein kinase (encoded byCCaMK) is a central component. AlthoughOryza sativaCCaMK(OsCCaMK) is required for fungal accommodation in rice roots, little is known about the role ofOsCCaMKin rice symbiosis with bacteria. Here, we report the effect of aTos17-inducedOsCCaMKmutant (NE1115) on CH4flux in low-nitrogen (LN) and standard-nitrogen (SN) paddy fields compared with wild-type (WT) Nipponbare. The growth of NE1115 was significantly decreased compared with that of the WT, especially in the LN field. The CH4flux of NE1115 in the LN field was significantly greater (156 to 407% in 2011 and 170 to 816% in 2012) than that of the WT, although no difference was observed in the SN field. The copy number ofpmoA(encodes methane monooxygenase in methanotrophs) was significantly higher in the roots and rhizosphere soil of the WT than in those of NE1115. However, themcrA(encodes methyl coenzyme M reductase in methanogens) copy number did not differ between the WT and NE1115. These results were supported by a13C-labeled CH4-feeding experiment. In addition, the natural abundance of15N in WT shoots (3.05‰) was significantly lower than in NE1115 shoots (3.45‰), suggesting greater N2fixation in the WT because of dilution with atmospheric N2(0.00‰). Thus, CH4oxidation and N2fixation were simultaneously activated in the root zone of WT rice in the LN field and both processes are likely controlled byOsCCaMK.

Sign in / Sign up

Export Citation Format

Share Document