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Bacterial communities associated with roots impact the health and nutrition of the host plant. The dynamics of these microbial assemblies over the plant life cycle are, however, not well understood. Here, we use dense temporal sampling of 1,510 samples from root spatial compartments to characterize the bacterial and archaeal components of the root-associated microbiota of field grown rice (Oryza sativa) over the course of 3 consecutive growing seasons, as well as 2 sites in diverse geographic regions. The root microbiota was found to be highly dynamic during the vegetative phase of plant growth and then stabilized compositionally for the remainder of the life cycle. Bacterial and archaeal taxa conserved between field sites were defined as predictive features of rice plant age by modeling using a random forest approach. The age-prediction models revealed that drought-stressed plants have developmentally immature microbiota compared to unstressed plants. Further, by using genotypes with varying developmental rates, we show that shifts in the microbiome are correlated with rates of developmental transitions rather than age alone, such that different microbiota compositions reflect juvenile and adult life stages. These results suggest a model for successional dynamics of the root-associated microbiota over the plant life cycle.

Allotetraploid cotton species are a vital source of spinnable fiber for textiles. The polyploid nature of the cotton genome raises many evolutionary questions as to the relationships between duplicated genomes. We describe the evolution of the cotton genome (SNPs and structural variants) with the greatly improved resolution of 34 deeply re-sequenced genomes. We also explore the evolution of homoeologous regions in the AT- and DT-genomes and especially the phenomenon of conversion between genomes. We did not find any compelling evidence for homoeologous conversion between genomes. These findings are very different from other recent reports of frequent conversion events between genomes. We also identified several distinct regions of the genome that have been introgressed between G. hirsutum and G. barbadense, which presumably resulted from breeding efforts targeting associated beneficial alleles. Finally, the genotypic data resulting from this study provides access to a wealth of diversity sorely needed in the narrow germplasm of cotton cultivars.

The Tri-Service Microbiome Consortium (TSMC) was created to foster and enhance cooperation, collaboration, and communication of microbiome research among Department of Defense (DoD) researchers and their collaborators. The 8th Annual TSMC Symposium was held in Colorado Springs, CO on 25–26 September 2024 and featured oral and poster presentations and discussions centered on microbiome-related topics within four broad thematic areas: 1) Surveillance; 2) Health and Performance; 3) Enablers; and 4) Remediation. Collectively this meeting promoted sharing of methods, experiments, and findings across DoD affiliated microbiome research and promoted future and ongoing collaborations. This report summarizes the proceedings of the 8th Annual TSMC Symposium.

The Tri-Service Microbiome Consortium (TSMC) was founded to enhance collaboration, coordination, and communication of microbiome research among DoD organizations and to facilitate resource, material and information sharing among consortium members, which includes collaborators in academia and industry. The 2023 annual symposium was a hybrid meeting held in Washington DC on 26–27 September 2023 concurrent with the virtual attendance, with oral and poster presentations and discussions centered on microbiome-related topics within five broad thematic areas: 1) Environmental Microbiome Characterization; 2) Microbiome Analysis; 3) Human Microbiome Characterization; 4) Microbiome Engineering; and 5) In Vitro and In Vivo Microbiome Models. Collectively, the symposium provided an update on the scope of current DoD and DoD-affiliated microbiome research efforts and fostered collaborative opportunities. This report summarizes the presentations and outcomes of the 7th annual TSMC symposium.

[This corrects the article DOI: 10.1371/journal.pgen.1006012.].

The Isles Dernieres Barrier Island Refuge in Louisiana, USA, constitutes a major colonial waterbird breeding site, and several restoration projects have been undertaken to sustain waterbird populations on the refuge. However, very little is known about food resources that colonial waterbirds depend on in the Gulf of Mexico. Royal (Thalasseus maximus) and Sandwich (T. sandvicensis) tern diet composition was investigated to determine important food resources during the breeding period. Regurgitated prey items in the 2013 and 2014 breeding seasons were used to compare diet composition, prey item frequency, and prey item mass among four groups: Royal Tern adults, Royal Tern chicks, Sandwich Tern adults, and Sandwich Tern chicks. The two most frequent prey items were Atlantic croaker (Micropogonias undulatus) and bay anchovy (Anchoa mitchilli). Royal Tern adults consumed significantly more Sciaenids than any other tern group, and Sandwich Tern adults consumed more Engraulids than any other tern group. Royal and Sandwich tern adults partitioned food resources by prey species and prey size, while chick diet showed more overlap in prey species composition. Royal and Sandwich tern diet closely reflected the species composition of trawls from nearby waters, suggesting opportunistic prey selection. The diets of both tern species contained a variety of demersal prey items indicating use of discards from local fisheries activities. Interactions between breeding waterbirds and fisheries in coastal Louisiana may be an important conservation consideration with profound implications on breeding abundance and breeding success of waterbirds.

Background Massive computational power is needed to analyze the genomic data produced by next-generation sequencing, but extensive computational experience and specific knowledge of algorithms should not be necessary to run genomic analyses or interpret their results. Findings We present BamBam, a package of tools for genome sequence analysis. BamBam contains tools that facilitate summarizing data from BAM alignment files and identifying features such as SNPs, indels, and haplotypes represented in those alignments. Conclusions BamBam provides a powerful and convenient framework to analyze genome sequence data contained in BAM files.

Understanding the composition, evolution, and function of the Gossypium hirsutum (cotton) genome is complicated by the joint presence of two genomes in its nucleus (AT and DT genomes). These two genomes were derived from progenitor A-genome and D-genome diploids involved in ancestral allopolyploidization. To better understand the allopolyploid genome, we re-sequenced the genomes of extant diploid relatives that contain the A1 (Gossypium herbaceum), A2 (Gossypium arboreum), or D5 (Gossypium raimondii) genomes. We conducted a comparative analysis using deep re-sequencing of multiple accessions of each diploid species and identified 24 million SNPs between the A-diploid and D-diploid genomes. These analyses facilitated the construction of a robust index of conserved SNPs between the A-genomes and D-genomes at all detected polymorphic loci. This index is widely applicable for read mapping efforts of other diploid and allopolyploid Gossypium accessions. Further analysis also revealed locations of putative duplications and deletions in the A-genome relative to the D-genome reference sequence. The approximately 25,400 deleted regions included more than 50% deletion of 978 genes, including many involved with starch synthesis. In the polyploid genome, we also detected 1,472 conversion events between homoeologous chromosomes, including events that overlapped 113 genes. Continued characterization of the Gossypium genomes will further enhance our ability to manipulate fiber and agronomic production of cotton.

Gull-billed Terns (Gelochelidon nilotica) have historically demonstrated variability in nest-site selection and reproductive success throughout their breeding range. However, few studies have investigated the breeding parameters of Gull-billed Tern populations on barrier islands in the northern Gulf of Mexico, USA. The main objective of this study was to investigate annual variability of breeding population size, hatching success, and causes of nest failure during eight breeding seasons (2009–2016). Annual variation was observed in colony sizes (Range = 1–68 nests), colony locations (among five islands), and hatching success (0–93%). Mean hatching success was 56% and flooding was the main cause of failure, accounting for 64% of all failed nests. Additionally, nest site habitat characteristics were compared between successful and unsuccessful Gull-billed Tern nests. Nest substrate composition differed between successful and failed nests, and successful nests were also associated with higher elevation, greater distance from the high tide line, and less vegetative cover. There was considerable variation in Gull-billed Tern breeding population size and hatching success, which may be attributable to the dynamic nature of barrier island habitats. Long-term monitoring is required to better understand the breeding dynamics of Gull-billed Terns, but conservation efforts should consider maintaining island habitats that are protected from flooding and have adequate nesting substrate, minimal vegetation, and limited disturbance from humans and predators.