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Whole genome sequence of the syntrophic benzoate-degrading bacterium, Syntrophus buswellii DSM 102354 T

The syntrophic obligate proton-reducing bacterium Syntrophus buswellii DSM 102354 T , isolated from anaerobic digester sludge, degrades benzoate and possibly hydrocinnamate (phenyl-3-propionate) when grown with a suitable hydrogenotrophic partner. The complete genome sequence data provide insight regarding aromatic compound degradation under thermodynamically limiting conditions when exogenous electron acceptors are absent.

Syntrophus

Genomic-based biosurveillance for avian influenza: whole genome sequencing from wild mallards sampled during autumn migration in 2022–2023 reveals a high co-infection rate on migration stopover site in Georgia

The Caucasus region, including Georgia, is an important intersection for migratory waterbirds, offering potential for avian influenza virus (AIV) transmission between populations from different geographic areas. In 2022 and 2023, wild ducks were sampled during autumn migration events in Georgia to study the genetic relationships and molecular characteristics of influenza strains. Sequencing and phylogenetic analysis were used to compare the sampled strains to reference sequences from Africa, Asia, and Europe, allowing assessment of genetic relationships and virus transmission between migratory birds. Protein language modeling identified potential co-infections. Of 225 duck samples, 128 tested positive for the influenza M gene. 55 influenza-positive samples underwent whole-genome sequencing, revealing significant diversity. Analysis of the hemagglutinin (HA) segment showed notable differences among subtypes. Most samples were H6N1 and H6N6, but co-infections with combinations like H6H3, N8N1, N6H9, N2N6, and H9H6/N1N2 were also identified. These findings demonstrate the high variability of influenza viruses in migratory waterbirds in Georgia, including a notable rate of co-infections. Some samples exhibited uncommon genetic characteristics compared to other strains from the same year, suggesting Georgia’s role as a mixing vessel for influenza viruses. This facilitates reassortment during co-infections and contributes to the genetic diversity observed across flyways.

59 BASIC BIOLOGICAL SCIENCES

Application of Whole Genome Sequencing and MALDI-TOF to the Identifcation of Bacillus Species Isolated from Cleanrooms at NASA Johnson Space Center

Astromaterial cleanrooms at NASA Johnson Space Center are built environments that hold samples, such as lunar rocks, from different space exploration missions. Bacillus sp. are frequently detected in routine microbial monitoring of these facilities. Since this, and related genera, can form endospores that can withstand harsh conditions, they could contaminate astromaterials. This could confound searches for extraterrestrial life. Whole genome sequencing (WGS) is widely used for identifying bacterial strains and tracking their source; however, WGS is expensive and time consuming. Matrix-assisted laser desorption ionization– time of flight mass spectrometry (MALDI-TOF) shows promise as a low-cost, rapid method of identifying strains of bacteria, but few studies have compared this proteomics method to WGS. To evaluate a high throughput method of tracking the source of contamination of this built environment, WGS and MALDI-TOF was conducted on 18 bacterial strains isolated from surfaces in astromaterials cleanrooms. WGS identified 14 Bacillus, 2 Paenibacillus, 1 Solibacillus and 1 Alcaligenes strains. These isolates showed similarity to strains commonly observed in spacecraft assembly cleanrooms at other facilities. Cluster analysis of mass spectra generated by MALDI-TOF grouped strains together that were greater than 94% similar to each other in terms of amino acid sequences of single copy core genes, as assessed by WGS. This suggests that MALDI-TOF and WGS results are consistent with each other and MALDI-TOF can rapidly identify strains of Bacillus sp. isolated from cleanroom environments with a resolution comparable to WGS. Based on phylogenomic analysis, these results also suggest the presence of a cosmopolitan class of Bacillus sp. that are more likely to be found in cleanrooms and similar built environments than in natural systems.

Farnaz Mazhari

Genome Sequences of Bacteria Isolated from the International Space Station Water Systems

We report draft genomes of five bacteria recovered from the United States and Russian water systems onboard the International Space Station: bacteria of the genera Ralstonia, Burkholderia, Cupriavidus, Methylobacterium, and Pseudomonas. These sequences will help further the understanding of water reclamation and environmental control and life support systems in space.

Christian L. Castro

Draft Genome Sequences of 14 Bacterial Isolates from the Rhizosphere of Bioenergy Sorghum

We report the draft genomes of a collection of 15 bacteria, isolated from the rhizosphere soil of bioenergy sorghum (Sorghum bicolor (L.) Moench). These isolates belong to the genera, Acidovorax, Nocardioides, Agrobacterium, Peribacillus, Caulobacter, Cupriavidus, Pseudomonas, Rhizobium, Sphingomonas, Priestia, Dyadobacter, Roseomonas, Ideonella, and Bacillus.

Black, Grace S.

Complete genome sequence of Luteolibacter sp. strain Populi, a member of phylum Verrucomicrobiota isolated from the Populus trichocarpa rhizosphere

Luteolibacter sp. strain Populi is a bacterium from the phylum Verrucomicrobiota, isolated from the rhizosphere of a black cottonwood tree, Populus trichocarpa, from the Cascade mountains in Washington. Its 6.6-Mb chromosome was completely sequenced using Oxford Nanopore long-read sequencing and is predicted to encode 5,301 proteins and 60 RNAs.

59 BASIC BIOLOGICAL SCIENCES

Complete genome sequence of Rhodococcus qingshengii phage Perlina

ABSTRACT Rhodococcus phage Perlina is a novel phage isolated on Rhodococcus qingshengii S10. Perlina encodes 112 open reading frames with typical phage structural genes identified and 3 tRNAs (tRNA-Ile, tRNA-Met, and tRNA-Asn). Few close relatives can be identified at the nucleotide level, suggesting a new phage species.

59 BASIC BIOLOGICAL SCIENCES

Develop High-Throughput Workflows for Whole-Genome Sequencing and Insertion Site Screening (CRADA Final Report)

The engineering of microbes for biomanufacturing (e.g. of fuels, chemicals, materials) applications has advanced to a stage where researchers screen genetic libraries with millions of variations each for those with enhanced productivity. This screening, however, can be slow and expensive, as screening individual variants in a high-throughput yet cost-effective manner is challenging. In this project, we aimed to reduce by 3-fold costs associated with the sequencing aspects of the screening process (to determine which genetic variant is responsible for an observed change in productivity), while being able to process over 1,000 samples per batch.

60 APPLIED LIFE SCIENCES

Develop High-Throughput Workflows for Whole-Genome Sequencing and Insertion Site Screening

The engineering of microbes for biomanufacturing (e.g. of fuels, chemicals, materials) applications has advanced to a stage where researchers screen genetic libraries with millions of variations each for those with enhanced productivity. This screening, however, can be slow and expensive, as screening individual variants in a high-throughput yet cost-effective manner is challenging. In this project, we aimed to reduce by 3-fold costs associated with the sequencing aspects of the screening process (to determine which genetic variant is responsible for an observed change in productivity), while being able to process over 1,000 samples per batch.

60 APPLIED LIFE SCIENCES

Resolution of Maldi-Tof Compared to Whole Genome Sequencing for Identification of Bacillus Species Isolated From Cleanrooms at Nasa Johnson Space Center

The Astromaterials Acquisition and Curation Office at NASA Johnson Space Center maintains cleanrooms to archive extraterrestrial materials returned from space exploration missions. Compared to typical built environments, oligotrophic conditions make these facilities inhospitable to microbes. Despite these controls, bacteria and fungi are regularly cultured from these cleanrooms. In particular, Bacillus sp. are frequently isolated during routine microbial monitoring. Endospores associated with this genus can survive extreme environments, such as cleanrooms. This microbial contamination may affect the integrity of astromaterials.

Microbiology

Molecular motors and their functions in plants

Molecular motors that hydrolyze ATP and use the derived energy to generate force are involved in a variety of diverse cellular functions. Genetic, biochemical, and cellular localization data have implicated motors in a variety of functions such as vesicle and organelle transport, cytoskeleton dynamics, morphogenesis, polarized growth, cell movements, spindle formation, chromosome movement, nuclear fusion, and signal transduction. In non-plant systems three families of molecular motors (kinesins, dyneins, and myosins) have been well characterized. These motors use microtubules (in the case of kinesines and dyneins) or actin filaments (in the case of myosins) as tracks to transport cargo materials intracellularly. During the last decade tremendous progress has been made in understanding the structure and function of various motors in animals. These studies are yielding interesting insights into the functions of molecular motors and the origin of different families of motors. Furthermore, the paradigm that motors bind cargo and move along cytoskeletal tracks does not explain the functions of some of the motors. Relatively little is known about the molecular motors and their roles in plants. In recent years, by using biochemical, cell biological, molecular, and genetic approaches a few molecular motors have been isolated and characterized from plants. These studies indicate that some of the motors in plants have novel features and regulatory mechanisms. The role of molecular motors in plant cell division, cell expansion, cytoplasmic streaming, cell-to-cell communication, membrane trafficking, and morphogenesis is beginning to be understood. Analyses of the Arabidopsis genome sequence database (51% of genome) with conserved motor domains of kinesin and myosin families indicates the presence of a large number (about 40) of molecular motors and the functions of many of these motors remain to be discovered. It is likely that many more motors with novel regulatory mechanisms that perform plant-specific functions are yet to be discovered. Although the identification of motors in plants, especially in Arabidopsis, is progressing at a rapid pace because of the ongoing plant genome sequencing projects, only a few plant motors have been characterized in any detail. Elucidation of function and regulation of this multitude of motors in a given species is going to be a challenging and exciting area of research in plant cell biology. Structural features of some plant motors suggest calcium, through calmodulin, is likely to play a key role in regulating the function of both microtubule- and actin-based motors in plants.

Non-NASA Center