Biology subjects

Mitchell, S. L.

Publications and source records attributed to Mitchell, S. L..

3 recordsLinked to original sources

bioRxiv2023

Penicillin-binding protein redundancy in Bacillus subtilis enables growth during alkaline shock

Penicillin-binding proteins (PBPs) play critical roles in cell wall construction, cell shape, and bacterial replication. Bacteria maintain a diversity of PBPs, indicating that despite their apparent functional redundancy, there is differentiation across the PBP family. Seemingly redundant proteins can be important for enabling an organism to cope with environmental stressors. We sought to evaluate the consequence of environmental pH on PBP enzymatic activity in Bacillus subtilis. Our data show that a subset of B. subtilis PBPs change activity levels during alkaline shock and that one PBP isoform is rapidly modified to generate a smaller protein (i.e., PBP1a to PBP1b). Our results indicate that a subset of the PBPs are preferred for growth under alkaline conditions, while others are readily dispensable. Indeed, we found that this phenomenon could also be observed in Streptococcus pneumoniae, implying that it may be generalizable across additional bacterial species and further emphasizing the evolutionary benefit of maintaining many, seemingly redundant periplasmic enzymes. O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=119 SRC="FIGDIR/small/533529v1_ufig1.gif" ALT="Figure 1"> View larger version (38K): org.highwire.dtl.DTLVardef@bf28c7org.highwire.dtl.DTLVardef@e2e88org.highwire.dtl.DTLVardef@1112259org.highwire.dtl.DTLVardef@1e604ae_HPS_FORMAT_FIGEXP M_FIG C_FIG

microbiology↗

bioRxiv2022

Logging alters tropical forest structure, while conversion reduces biodiversity and functioning

The impacts of degradation and deforestation on tropical forests are poorly understood, particularly at landscape scales. We present an extensive ecosystem analysis of the impacts of logging and conversion of tropical forest to oil palm from a large-scale study in Borneo, synthesizing responses from 82 variables categorized into four ecological levels spanning a broad suite of ecosystem properties: 1) structure and environment, 2) species traits, 3) biodiversity, and 4) ecosystem functions. Responses were highly heterogeneous and often complex and non-linear. Variables that were directly impacted by the physical process of timber extraction, such as soil structure, were sensitive to even moderate amounts of logging, whereas measures of biodiversity and ecosystem functioning were generally resilient to logging but more affected by conversion to oil palm plantation. One-Sentence SummaryLogging tropical forest mostly impacts structure while biodiversity and functions are more vulnerable to habitat conversion.

ecology↗

bioRxiv2020

Capturing biodiversity complexities while accounting for imperfect detection: the application of occupancy-based diversity profiles.

O_LIMeasuring the multidimensional diversity properties of a community is of great importance for ecologists, conservationists and stakeholders. Diversity profiles, a plotted series of Hill numbers, simultaneously capture all the common diversity indices. However, diversity metrics require information on species abundance. They often rely on raw count data without accounting for imperfect and varying detection, although detectability can vary between species and study sites. Hierarchical occupancy models explicitly account for variation in detectability, and Hill numbers have been expanded to allow estimation based on occupancy probability. But agreement between occupancy and abundance-based diversity profiles has not been investigated. C_LIO_LIHere, we fit community occupancy models to simulated animal communities to explore how well occupancy-based diversity profiles reflect true abundance-based diversity. Because we expect occupancy-based diversity to be overestimated, we further tested a novel occupancy thresholding approach to reduce potential biases in the estimated diversity profiles. Finally, we use empirical data from a megadiverse bird community to present how the framework can be extended to consider trait or phylogeny-based similarity when calculating diversity profiles. C_LIO_LIThe simulation study showed that occupancy-based diversity profiles produced among-community patterns in diversity similar to true abundance diversity profiles, although within-community diversity was overestimated with the exception of richness. While applying an occupancy threshold reduced this positive bias, this resulted in negative bias in species richness estimates and slightly reduced the ability to reproduce true differences among the simulated communities. Application of our approach to a large bird dataset revealed differential diversity patterns in communities of different habitat types. Accounting for phylogenetic and ecological similarities between species reduced diversity and its variability among habitats. C_LIO_LIOur framework allows investigating the complexity of diversity for incidence data, while accounting for imperfect and varying detection probabilities, as well as species similarities. Visualizing results in the form of diversity profiles facilitates comparison of diversity between sites or across time. Therefore, our extension to the diversity profile framework will be a useful tool for studying and monitoring biodiversity. C_LI

ecology↗