Biology subjects

Shapiro, N.

Publications and source records attributed to Shapiro, N..

6 recordsLinked to original sources

bioRxiv2024

Red seaweed supplementation suppresses methanogenesis in the rumen, revealing potentially advantageous traits among hydrogenotrophic bacteria

Macroalgae belonging to the genus Asparagopsis have been shown to reduce the production of methane (CH4) during rumen fermentation, while increasing feed efficiency when added to the feed of cattle. However, little is known about how the microbial community in the rumen responds to Asparagopsis supplementation, and how changes in the rumen microbiome may contribute to shifts in rumen function and ultimately the hosts phenotype. In this study, we generated and analyzed metagenomic and metatranscriptomic data from the microbiome associated with rumen fluid collected from two cohorts of lactating dairy cows, one fed a diet supplemented with Asparagopsis armata (treatment) and another fed the same diet without A. armata supplementation (control). The reduction of CH4 emission from animals that received A. armata was coupled to a qualitative decrease in relative archaeal abundance and a significant reduction in the transcription of methanogenesis pathways. Additionally, a significant decrease in the transcription of genes for complex carbon catabolism and a re-organization of the expression profile of carbon catabolic genes at the species level was observed in treated animals. Increased H2 production, a consequence of methanogenesis suppression, was coupled to a significant increase in the transcription of hydrogenases that mediate hydrogenotrophic metabolism in the treatment group. Analysis of metatranscriptome data identified a single uncultured hydrogenotrophic bacterial species (a Duodenibacillus sp.) as the dominant driver of this transcriptional change. Comparative genomic analysis between the Duodenibacillus sp. and other hydrogenotrophic rumen organisms revealed metabolic traits in the Duodenibacillus that may provide a competitive advantage in H2 scavenging. These findings provide an initial understanding of how rumen microbiota respond to a promising CH4 reducing feed additive, and may serve as a model to understand alternative stable rumen microbiome states that produce less methane and increase animal productivity.

microbiology↗

bioRxiv2022

Ethanol Exposure Perturbs Sea Urchin Development and Disrupts Developmental Timing

Ethanol is a known vertebrate teratogen that causes craniofacial defects as a component of fetal alcohol syndrome (FAS). Our results show that sea urchin embryos treated with ethanol similarly show broad skeletal patterning defects, potentially analogous to the defects associated with FAS. The sea urchin larval skeleton is a simple patterning system that involves only two cell types: the primary mesenchymal cells (PMCs) that secrete the calcium carbonate skeleton and the ectodermal cells that provide migratory, positional, and differentiation cues for the PMCs. Perturbations in RA biosynthesis and Hh signaling pathways are thought to be causal for the FAS phenotype in vertebrates. Surprisingly, our results indicate that these pathways are not functionally relevant for the teratogenic effects of ethanol in developing sea urchins. We found that developmental morphology as well as the expression of ectodermal and PMC genes was delayed by ethanol exposure. Temporal transcriptome analysis revealed significant impacts of ethanol on signaling and metabolic gene expression, and a disruption in the timing of GRN gene expression that includes both delayed and precocious gene expression throughout the specification network. We conclude that the skeletal patterning perturbations in ethanol-treated embryos likely arise from a loss of temporal synchrony within and between the instructive and responsive tissues.

developmental biology↗

bioRxiv2021

DNA methylation patterns in bacteria of the genus Ensifer during free living growth and during nitrogen-fixing symbiosis with Medicago spp.

Methylation of specific DNA sequences is ubiquitous in bacteria and has known roles in immunity and regulation of cellular processes, such as the cell cycle. Using single-molecule real-time sequencing, six genome-wide methylated motifs were identified across four Ensifer strains, five of which were strain-specific. Only the GANTC motif, recognized by the cell cycle-regulated CcrM methyltransferase, was methylated in all strains. In actively dividing cells, methylation of GANTC motifs increased progressively from the ori to ter regions in each replicon, in agreement with a cell cycle-dependent regulation of CcrM. In contrast, there was near full genome-wide GANTC methylation in the early stage of symbiotic differentiation. This was followed by a moderate decrease in the overall extent methylation and a progressive decrease in chromosomal GANTC methylation from the ori to ter regions in later stages of differentiation. We interpret these observations as evidence of dysregulated and constitutive CcrM activity during terminal differentiation, and we hypothesize that it is a driving factor for endoreduplication of terminally differentiated bacteroids.

microbiology↗

bioRxiv2019

Impact of soil salinity on the cowpea nodule-microbiome and the isolation of halotolerant PGPR strains to promote plant growth under salinity stress

Four soil samples (SS-1--SS-4) isolated from semi-arid soils in Punjab, Pakistan were used as inocula for cowpea (Vigna unguiculata L.) grown under salinity stress to analyze the composition of bacteria in the rhizosphere and within nodules through cultivation-dependent and cultivation-independent methods. Two cowpea varieties, 603 and the salt-tolerant CB 46, were each inoculated with four different native soil samples, and data showed that plants inoculated with soil samples SS-2 and SS-4 grew better than plants inoculated with soil samples SS-1 and SS-3. Bacteria were isolated from both soils and nodules, and 34 of the 51 original isolates tested positive for PGPR traits in plate assays with many exhibiting multiple plant growth-promoting properties. A number of isolates were positive for all PGPR traits tested. For the microbiome studies, environmental DNA (eDNA) was isolated from SS-1 and SS-4, which represented the extremes of the Pakistan soils to which the plants responded, and by 16S rRNA gene sequencing analysis were found to consist mainly of Actinobacteria, Firmicutes, and Proteobacteria. However, sequencing analysis of eDNA isolated from cowpea nodules established by the trap plants grown in the four Pakistan soils indicated that the nodule microbiome consisted almost exclusively of Proteobacterial sequences, particularly Bradyrhizobium. Yet, many other bacteria including Rhizobium, Mesorhizobium, Pseudomonas, as well as Paenibacillus, Bacillus as well as non-proteobacterial genera were isolated from the nodules of soil-inoculated cowpea plants. This discrepancy between the bacteria isolated from cowpea nodules (Proteobacteria and non-Proteobacteria) versus those detected in the nodule microbiome (Proteobacteria) needs further study.

plant biology↗

bioRxiv2018

Community structure of phototrophic co-cultures from extreme environments

Cyanobacteria are found in most illuminated environments and are key players in global carbon and nitrogen cycling. Although significant efforts have been made to advance our understanding of this important phylum, still little is known about how members of the cyanobacteria affect and respond to changes in complex biological systems. This lack of knowledge is in part due to our dependence on pure cultures when determining the metabolism and function of a microorganism. In the work presented here we took advantage of the Culture Collection of Microorganisms from Extreme Environments (CCMEE), a collection of more than 1,000 publicly available photosynthetic co-cultures now maintained at the Pacific Northwest National Laboratory. To highlight some of their scientific potential, we selected 26 of these photosynthetic co-cultures from the CCMEE for 16S rRNA gene sequencing. We assessed if samples readily available from the CCMEE could be used to generate new insights into the role of microbial communities in global and local carbon and nitrogen cycling. Results from this work support the existing notion that culture depositories in general hold the potential to advance fundamental and applied research. If collections of co-cultures can be used to infer roles of the individual organisms remains to be seen and requires further investigation.

microbiology↗

bioRxiv2017

Critical Assessment of Metagenome Interpretation - a benchmark of computational metagenomics software

In metagenome analysis, computational methods for assembly, taxonomic profiling and binning are key components facilitating downstream biological data interpretation. However, a lack of consensus about benchmarking datasets and evaluation metrics complicates proper performance assessment. The Critical Assessment of Metagenome Interpretation (CAMI) challenge has engaged the global developer community to benchmark their programs on datasets of unprecedented complexity and realism. Benchmark metagenomes were generated from ~700 newly sequenced microorganisms and ~600 novel viruses and plasmids, including genomes with varying degrees of relatedness to each other and to publicly available ones and representing common experimental setups. Across all datasets, assembly and genome binning programs performed well for species represented by individual genomes, while performance was substantially affected by the presence of related strains. Taxonomic profiling and binning programs were proficient at high taxonomic ranks, with a notable performance decrease below the family level. Parameter settings substantially impacted performances, underscoring the importance of program reproducibility. While highlighting current challenges in computational metagenomics, the CAMI results provide a roadmap for software selection to answer specific research questions.

bioinformatics↗