Biology subjects

Howe, A. C.

Publications and source records attributed to Howe, A. C..

6 recordsLinked to original sources

bioRxiv2024

Bacteria in honeybee crops are decoupled from those in floral nectar and bee mouths

Bacteria in the honeybee gut are a well-recognized factor affecting bee health. However, the primary focus of this research has been the hindgut, while the crop, or honey stomach, is assumed to be dominated by environmentally acquired transient taxa that matter little to the bees. To evaluate this assumption, we examined bacterial taxa in the crop and mouth of Apis mellifera and A. cerana japonica foragers and in the nectar of Prunus mume flowers visited by the bees in the Minabe-Tanabe region of Japan. We found that in bacterial composition, the crop was distinct from both the mouth and the nectar, whereas mouth and nectar samples were indistinguishable. Furthermore, the crop remained similar in bacterial composition and diversity, while the mouth showed a sharp drop in alpha diversity and a large increase in beta diversity, from summer to winter. These results refute the conventional assumption, suggesting instead that the crop contains a conserved bacterial community largely distinct from environmental taxa. We also found that strains of a crop-associated species, Apilactobacillus kunkeei, could be season- and host species-specific. Together, these findings suggest that crop-associated bacterial communities should be studied further to better understand the relationship between honeybees and their gut bacteria.

ecology↗

bioRxiv2023

Litter Matters: The Importance of Decomposition Products for Soil Bacterial Diversity and abundance of key groups of the N cycle in Tropical Areas

This study investigated the contribution of soil organic layers to bacterial diversity evaluations. We used a forest in the eastern Amazon and an adjacent pasture as model systems. Distinct organic and organo-mineral layers were identified in the forest and pasture floors, including the litter, partially and wholly decomposed organic material, and the mineral and rhizospheric soils. DNA was extracted, and 16S rRNA gene sequencing and qPCR were performed to assess bacterial community structure and the abundance of critical groups of the N cycle. We observed a clear vertical gradient in bacterial community composition. Species followed a log-normal distribution, with the highest richness and diversity observed in transitional organic layers of both land uses. Generally, critical groups of the N cycle were more abundant in these transitional layers, especially in the pastures fragmented litter and in the forests partially decomposed organic material. Considering the organic layers increased diversity estimates significantly, with the highest alpha and gamma bacterial diversity observed on the pasture floor and the highest beta diversity on the forest floor. The results show that organic layers harbor significant bacterial diversity in natural and anthropized systems and suggest that they can be crucial for maintaining the N cycle in these ecosystems, highlighting the need to consider them when studying soil bacterial diversity.

microbiology↗

bioRxiv2021

Response of total (DNA) and metabolically active (RNA) microbial communities in Miscanthus x giganteus cultivated soil to different nitrogen fertilization rates

Miscanthus x giganteus is a promising high-yielding perennial plant to meet growing bioenergy demands but the degree to which the soil microbiome affects its nitrogen cycling and subsequently, biomass yield remains unclear. In this study, we hypothesize that contributions of metabolically active soil microbial membership may be underestimated with DNA-based approaches. We assessed the response of the soil microbiome to nitrogen availability in terms of both DNA and RNA soil microbial communities from the Long-term Assessment of Miscanthus Productivity and Sustainability (LAMPS) field trial. DNA and RNA were extracted from 271 samples, and 16S SSU rRNA amplicon sequencing was performed to characterize microbial community structure. Significant differences were observed in the resulting soil microbiomes and were best explained by the sequencing library of origin, either DNA and RNA. Similar numbers of taxa were detected in DNA and RNA microbial communities, with more than 90% of taxa shared. However, the profile of dominant taxa within DNA and RNA differed, with varying proportions of Actinobacteria and Proteobacteria and Firmicutes and Proteobacteria. Only RNA microbial communities showed seasonal responses to nitrogen fertilization, and these differences were associated with nitrogen-cycling bacteria. The relative abundance of bacteria associated with nitrogen cycling was 7-folds higher in RNA than in DNA, and genes associated with denitrifying bacteria were significantly enriched in RNA, suggesting that these bacteria may be underestimated with DNA-only approaches. Our findings indicate that RNA-based SSU characterization can be a significant and complementing resource for understanding the role of soil microbiomes in bioenergy crop production. ImportanceMiscanthus x giganteus is becoming a cornerstone of bioeconomy cropping systems, but it remains unclear how the soil microbiome supplies nitrogen to this low-input crop. DNA-based techniques are used to provide community characterization but may miss important metabolically active taxa. By analyzing both DNA- and actively transcribed RNA-based microbial communities, we found that nitrogen cycling taxa in the soil microbiome may be underestimated using only DNA-based approaches. Accurately understanding the role of microbes and how they cycle nutrients is important for the development of sustainable bioenergy crops, and RNA-based approaches are recommended as a complement to DNA approaches to better understand the microbial, plant, and management interactions.

microbiology↗

bioRxiv2021

Genome-centric analyses of seasonal phyllosphere microbiome activities in perennial crops

Plants and microorganisms form beneficial associations. Understanding plant-microbe interactions will inform microbiome management to enhance crop productivity and resilience to stress. Here, we apply a genome-centric approach to identify key leaf microbiome members on field-grown switchgrass and miscanthus, and quantify their activities for switchgrass over two growing seasons. We integrate metagenome and metatranscriptome sequencing from 192 leaf samples collected over key time points in crop phenology. We curated 40 focal metagenome-assembled-genomes (MAGs) and conservatively focus analysis on transcript recruitment to medium and high-quality MAGs that were <10% contaminated and >50% complete. Classes represented by these MAGs (Actinomycetia, Alpha- and Gamma-Proteobacteria, and Bacteroidota) were active and had seasonal dynamics in key functions, including enrichments in transcripts for of short chain dehydrogenase, molybdopterin oxioreductase, and polyketide cyclase in the late season. The majority of MAGs had activated stress-associated pathways, including trehalose metabolism, indole acetic acid degradation, betaine biosynthesis, and reactive oxygen species degradation, suggesting direct engagement with the host environment. We also detected seasonally activated biosynthetic pathways for terpenes (carotenoid and isoprenoids), and for various non-ribosomal peptide pathways that were poorly annotated. Overall, this study overcame laboratory and bioinformatic challenges associated with field-based leaf metatranscriptome analysis to inform potential key activities of these phyllosphere populations. These activities collectively support that leaf-associated bacterial populations are seasonally dynamic, responsive to host cues and interactively engage in feedbacks with the plant.

microbiology↗

bioRxiv2019

Strategies for building computing skills to support microbiome analysis: a five-year perspective from the EDAMAME workshop

Here, we report our educational approach and learner evaluations of the first five years of the Explorations in Data Analysis for Metagenomic Advances in Microbial Ecology (EDAMAME) workshop, held annually at Michigan State Universitys Kellogg Biological Station from 2014-2018. We hope this information will be useful for others who want to organize computing-intensive workshops and encourage quantitative skill development among microbiologists.\n\nImportanceHigh-throughput sequencing and related statistical and bioinformatic analyses have become routine in microbiology in the past decade, but there are few formal training opportunities to develop these skills. A week-long workshop can offer sufficient time for novices to become introduced to best computing practices and common workflows in sequence analysis. We report our experiences in executing such a workshop targeted to professional learners (graduate students, post-doctoral scientists, faculty, and research staff).

scientific communication and education↗

bioRxiv2018

RefSoil+: A reference for antimicrobial resistance genes on soil plasmids

Plasmids harbor transferable genes that contribute to the functional repertoire of microbial communities, yet their contributions to metagenomes are often overlooked. Environmental plasmids have the potential to spread antibiotic resistance to clinical microbial strains. In soils, high microbiome diversity and high variability in plasmid characteristics present a challenge for studying plasmids. To improve understanding of soil plasmids, we present RefSoil+, a database containing plasmid sequences from 922 soil microorganisms. Soil plasmids were relatively larger than other described plasmids, which is a trait associated with plasmid mobility. There was no relationship between chromosome size and plasmid size or number, suggesting that these genomic traits are independent in soil. Soil-associated plasmids, but not chromosomes, had fewer antibiotic resistance genes than other microorganisms. These data suggest that soils may offer limited opportunity for plasmid-mediated transfer of described antibiotic resistance genes. RefSoil+ can serve as a baseline for the diversity, composition, and host-associations of plasmid-borne functional genes in soil, a utility that will be enhanced as the database expands. Our study improves understanding of soil plasmids and provides a resource for assessing the dynamics of the genes that they carry, especially genes conferring antibiotic resistances.\n\nImportanceSoil-associated plasmids have the potential to transfer antibiotic resistance genes from environmental to clinical microbial strains, which is a public health concern. A specific resource is needed to aggregate knowledge of soil plasmid characteristics so that the content, host-associations, and dynamics of antibiotic resistance genes can be assessed and then tracked between the environment and the clinic. Here, we present RefSoil+, a database of soil-associated plasmids. RefSoil+ presents a contemporary snapshot of antibiotic resistance genes in soil that can serve as a reference as novel plasmids and transferred antibiotic resistances are discovered. Our study broadens our understanding of plasmids in soil and provides a community resource for investigating clinic-environment dynamics of important plasmid-associated genes, including antibiotic resistance genes.

microbiology↗