Lag phase represents the earliest and most poorly understood stage of the bacterial growth cycle. We developed a reproducible experimental system and conducted functional genomic and physiological analyses of a 2-h lag phase in Salmonella enterica serovar Typhimurium. Adaptation began within 4 min of inoculation into fresh LB medium with the transient expression of genes involved in phosphate uptake. The main lag-phase transcriptional program initiated at 20 min with the upregulation of 945 genes encoding processes such as transcription, translation, iron-sulfur protein assembly, nucleotide metabolism, LPS biosynthesis, and aerobic respiration. ChIP-chip revealed that RNA polymerase was not "poised" upstream of the bacterial genes that are rapidly induced at the beginning of lag phase, suggesting a mechanism that involves de novo partitioning of RNA polymerase to transcribe 522 bacterial genes within 4 min of leaving stationary phase. We used inductively coupled plasma mass spectrometry (ICP-MS) to discover that iron, calcium, and manganese are accumulated by S. Typhimurium during lag phase, while levels of cobalt, nickel, and sodium showed distinct growth-phase-specific patterns. The high concentration of iron during lag phase was associated with transient sensitivity to oxidative stress. The study of lag phase promises to identify the physiological and regulatory processes responsible for adaptation to new environments.
Biological invasions are a form of global change threatening biodiversity, ecosystem stability, and human health, and cost government agencies billions of dollars in remediation and eradication programs. Attempts to eradicate introduced species are most successful when detection of newly established populations occurs early in the invasion process. We review existing and emerging tools -specifically environmental DNA (eDNA), chemical approaches, remote sensing, citizen science, and agency-based monitoring -for surveillance and monitoring of invasive species. For each tool, we consider the benefits provided, examine challenges and limitations, discuss data sharing and integration, and suggest best practice implementations for the early detection of invasive species. Programs that promote public participation in large-scale biodiversity identification and monitoring (such as iNaturalist and eBird) may be the best resources for early detection. However, data from these platforms must be monitored and used by agencies that can mount appropriate response efforts. Control efforts are more likely to succeed when they are focused on early detection and prevention, thereby saving considerable time and resources.
Environmental DNA (eDNA) is DNA extracted from environmental samples (e.g. water) that can be used to infer presence or abundance of species, sometimes with greater sensitivity than conventional sampling methods. Previous eDNA applications to lotic ecosystems have shown promise in accurately inferring species presence, although studies attempting to estimate species abundance have had mixed results. This may be because eDNA applications in lotic environments are challenged by directional streamflow, which has the potential to transport detectable eDNA downstream from its source. Our study sought to evaluate whether results from eDNA corresponded well with the presence and abundance of the narrowly endemic, large river specialist crayfish Faxonius eupunctus obtained through a rigorous, well‐tested conventional sampling method, or instead, if downstream eDNA transport in this large river system might overwhelm the effect of local species abundance. We used a species‐specific quantitative PCR (qPCR) assay to amplify F. eupunctus eDNA collected in surface water samples from streams within the Eleven Point River drainage, Arkansas and Missouri, U.S.A. We estimated F. eupunctus eDNA detection probabilities and examined relationships between eDNA detection probability and site‐scale variables using a hierarchical occupancy and detection probability modelling framework. Results from eDNA sampling showed ˜90% agreement relative to our conventional sampling method in estimating F. eupunctus presence, although eDNA failed to detect F. eupunctus eDNA at two upstream sites where conventional sampling detected F. eupunctus individuals. We found a poor relationship between F. eupunctus eDNA detection probability and local F. eupunctus abundance, and a strong relationship between eDNA detection probability and upstream river distance, which we used as a proxy for the risk of downstream transport of eDNA from upstream F. eupunctus populations. Our results demonstrate eDNA is a largely reliable tool for estimating the presence of benthic organisms in large, freshwater rivers. However, the likelihood of detecting F. eupunctus eDNA presence in our study increased as we moved down the stream network, even though local species abundances were greatest at more upstream locations. Therefore, the ability of eDNA to accurately reflect species presence or abundance in some lotic environments may be hindered by the downstream transport of detectable eDNA.
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