Biology subjects

Thompson, F. L.

Publications and source records attributed to Thompson, F. L..

4 recordsLinked to original sources

bioRxiv2022

DISSECTING LIGHT SENSING AND METABOLIC PATHWAYS ON THE MILLIMETER SCALE IN HIGH-ALTITUDE MODERN STROMATOLITES

Modern non-lithifying stromatolites (STs) on the shore of the volcanic lake Socompa in the Puna are affected by several extreme conditions. Although STs were proposed as ecologic models for understanding stress response and resilience in microbial ecosystems constituting a window into the past, our knowledge of ST function is still nascent. The present study assesses for the first time light utilization and functional metabolic stratification of STs on a millimeter scale through shotgun metagenomics. In addition, a scanning-electron-microscopy approach was used to explore the community. Our results demonstrated that Bacteroidetes and Cyanobacteria play major roles as ST builders and primary producers to sustain a diverse community of heterotrophs. STs manifest a high occurrence of genes for the synthesis of UV-protecting pigments, the cryptochrome-photolyase family (CPF), and rhodopsins in the surface layers. Three different ecologic niches involving the use of light in energy production were defined. Calvin-Benson and Wood-Ljungdahl pathways were proposed as the main mechanisms for carbon fixation. Several genes account for the microelectrode chemical data and pigment measurements performed in previous publications. We also provide here an explanation for the vertical microbial mobility within the ST described previously. Finally, our study points to STs as ideal modern analogues of ancient STs.

ecology↗

bioRxiv2020

Insights on the taxonomy and ecogenomics of the Synechococcus collective

The genus Synechococcus (also named Synechococcus collective, SC) is a major contributor to global primary productivity. It is found in a wide range of aquatic ecosystems. Synechococcus is metabolically diverse, with some lineages thriving in polar and nutrient-rich locations, and other in tropical riverine waters. Although many studies have discussed the ecology and evolution of Synechococcus, there is a paucity of knowledge on the taxonomic structure of SC. Only a few studies have addressed the taxonomy of SC, and this issue still remains largely ignored. Our aim was to establish a new classification system for SC. Our analyses included comparing GC% content, genome size, pairwise Average Amino acid Identity (AAI) values, phylogenomics and gene cluster profiles of 170 publicly available SC genomes. All analyses were consistent with the discrimination of 11 genera, from which 2 are newly proposed (Lacustricoccus and Synechospongium). The new classification is also consistent with the habitat distribution (seawater, freshwater and thermal environments) and reflects the ecological and evolutionary relationships of SC. We provide a practical and consistent classification scheme for the entire Synechococcus collective.

microbiology↗

bioRxiv2020

Unlocking the genomic taxonomy of the Prochloroccus collective

Prochlorococcus is the most abundant photosynthetic prokaryote on our planet. The extensive ecological literature on the Prochlorococcus collective (PC) is based on the assumption that it comprises one single genus comprising the species Prochlorococcus marinus, containing itself a collective of ecotypes. Ecologists adopt the distributed genome hypothesis of an open pan-genome to explain the observed genomic diversity and evolution patterns of the ecotypes within PC. Novel genomic data for the PC prompted us to revisit this group, applying the current methods used in genomic taxonomy. As a result, we were able to distinguish the five genera: Prochlorococcus, Eurycolium, Prolificoccus, Thaumococcus and Riococcus. The novel genera have distinct genomic and ecological attributes.

microbiology↗

bioRxiv2018

Emergence of the East-Central-South-African genotype of Chikungunya virus in Brazil and the city of Rio de Janeiro may have occurred years before surveillance detection

Brazil, which is hyperendemic for dengue virus (DENV), has had recent Zika (ZIKV) and (CHIKV) Chikungunya virus outbreaks. Since March 2016, CHIKV is the arbovirus infection most frequently diagnosed in Rio de Janeiro. In the analysis of 1835 syndromic patients, screened by real time RT-PCR, 56.4% of the cases were attributed to CHIKV, 29.6% to ZIKV, and 14.1% to DENV-4. Sequence analyses of CHIKV from sixteen samples revealed that the East-Central-South-African (ECSA) genotype of CHIKV has been circulating in Brazil since 2013 [95% bayesian credible interval (BCI): 03/2012-10/2013], almost a year before it was detected by arbovirus surveillance program. Brazilian cases are related to Central African Republic sequences from 1980s. To the best of our knowledge, given the available sequence published here and elsewhere, the ECSA genotype was likely introduced to Rio de Janeiro early on 2014 (02/2014; BCI: 07/2013-08/2014) through a single event, after primary circulation in the Bahia state at the Northestern Brazil in the previous year. The observation that the ECSA genotype of CHIKV was circulating undetected underscores the need for improvements in molecular methods for viral surveillance.

genomics↗