Biology is designed for multi-semester biology courses for science majors. It is grounded on an evolutionary basis and includes exciting features that highlight careers in the biological sciences and everyday applications of the concepts at hand. To meet the needs of today’s instructors and students, some content has been strategically condensed while maintaining the overall scope and coverage of traditional texts for this course. Instructors can customize the book, adapting it to the approach that works best in their classroom. Biology also includes an innovative art program that incorporates critical thinking and clicker questions to help students understand—and apply—key concepts.

Biology is designed for multi-semester biology courses for science majors. It is grounded on an evolutionary basis and includes exciting features that highlight careers in the biological sciences and everyday applications of the concepts at hand. To meet the needs of today’s instructors and students, some content has been strategically condensed while maintaining the overall scope and coverage of traditional texts for this course. Instructors can customize the book, adapting it to the approach that works best in their classroom. Biology also includes an innovative art program that incorporates critical thinking and clicker questions to help students understand—and apply—key concepts.

This resource is a video abstract of a research paper created by Research Square on behalf of its authors. It provides a synopsis that's easy to understand, and can be used to introduce the topics it covers to students, researchers, and the general public. The video's transcript is also provided in full, with a portion provided below for preview:

"Microbiomes are more than just prokaryotes and viruses; they also contain important eukaryotes, including fungi and protists. However, eukaryotes are difficult to study using ‘shotgun’ metagenomics, as their signal is often overwhelmed by the prokaryotes. Some methods use eukaryote-specific marker genes, but they can’t detect eukaryotes that aren’t in the reference marker gene set, and such methods are not compatible with web-based tools for downstream analysis. But CORRAL (Clustering Of Related Reference ALignments) is designed to close those gaps. CORRAL identifies eukaryotes in metagenomic data based on alignments to eukaryote-specific marker genes and Markov clustering. It can detect microbial eukaryotes that are not included in the marker gene reference set. The process is even automated and can be carried out at scale. A recent paper demonstrates CORRAL’s sensitivity and accuracy with simulated datasets, mock community standards, and human microbiome datasets..."

The rest of the transcript, along with a link to the research itself, is available on the resource itself.

This includes materials to be used for a General Biology II course (or Introduction to Biology II course) for non-science majors.

This resource is a video abstract of a research paper created by Research Square on behalf of its authors. It provides a synopsis that's easy to understand, and can be used to introduce the topics it covers to students, researchers, and the general public. The video's transcript is also provided in full, with a portion provided below for preview:

"The ribosomal RNA (rRNA) gene approach to sequencing genetic material has revolutionized microbiome science. But it isn’t perfect. The method relies on the assumption that counts of rRNA genes translate into microbial abundance. Exceptions to that rule, however, are known, such as the observation that rRNA gene counts can be higher in fast-growing microbes. Now, researchers report a new relationship between rRNA genes and cell volume that could help correct for biases inherent to microbiome studies. An analysis of previously reported data showed that the number of 16S or 18S RNA genes per cell follows an allometric power law of cell volume. Applying this relationship to a dataset for bacteria found in intertidal rocks allowed for more accurate biovolume and cell count distributions to be estimated for all taxa detected. The development of more comprehensive cell-size databases could help strengthen the bias-correcting relationship and boost the power of current microbiome analyses..."

The rest of the transcript, along with a link to the research itself, is available on the resource itself.

This resource is a video abstract of a research paper created by Research Square on behalf of its authors. It provides a synopsis that's easy to understand, and can be used to introduce the topics it covers to students, researchers, and the general public. The video's transcript is also provided in full, with a portion provided below for preview:

"Natural microbial systems are all around us, from nutrient-rich soil to churning seawater to our own bodies. These complex systems include bacteria, archaea, viruses, and microbial eukaryotes. One of the best methods available for analyzing these systems is shotgun sequencing, which generates vast quantities of DNA sequence data. However, current data annotation methods don't include a dedicated way to find eukaryotic sequences. Now, researchers have introduced a bioinformatics method called EukDetect. EukDetect uses a database of over 500,000 universal marker genes from 241 conserved gene families across thousands of eukaryotes. Broad taxonomic coverage and accurate identification of low-abundance and high-similarity sequences were possible with EukDetect, and bacterial contamination was no obstacle to identifying eukaryotic species. EukDetect highlights information that could be missed or obscured in standard shotgun sequence analysis..."

The rest of the transcript, along with a link to the research itself, is available on the resource itself.

Welcome to the Teachers' Corner of Small Things Considered. In this section, we include the posts we deem most adequate for teaching purposes. We have reorganized them into subject areas geared for a typical microbiology course. To date, this material has been used for various forms of intellectual enrichment, e.g., suggested readings, class presentations, a source of topics for term papers. You can also find here our Talmudic Questions, which we characterize as those whose answers cannot be found in Google. We are told that some of these questions have been used in exams ranging from tests for undergraduate courses to qualifying/prelims for graduate students.

This resource is a video abstract of a research paper created by Research Square on behalf of its authors. It provides a synopsis that's easy to understand, and can be used to introduce the topics it covers to students, researchers, and the general public. The video's transcript is also provided in full, with a portion provided below for preview:

"Wastewater treatment plants are a critical piece of infrastructure that depend on microbes, both resident and incoming. Incoming microbes can be beneficial but may include parasites that need to be removed. Resident microbes, meanwhile, help break down organic waste. While much is known about bacteria in wastewater treatment plants, eukaryotes are frequently overlooked. Recently, researchers examined the whole microbiome of 10 wastewater treatment plants in Switzerland. They utilized metagenomics to measure which microbes were present and metatranscriptomics to analyze their activity. Bacteria were the most numerous— but eukaryotes, particularly protists, showed the most activity, and there was a surprising number and range of active parasites, which were particularly prevalent in the inflow. Network analysis suggested predation by resident microbes likely helped remove parasites..."

The rest of the transcript, along with a link to the research itself, is available on the resource itself.

This resource is a video abstract of a research paper created by Research Square on behalf of its authors. It provides a synopsis that's easy to understand, and can be used to introduce the topics it covers to students, researchers, and the general public. The video's transcript is also provided in full, with a portion provided below for preview:

"Microbial life can be found in nearly every environment on earth. These tiny organisms can significantly impact their surroundings, be it deep-sea microbes influencing the ecology of the ocean floor or the human gut microbiome affecting health. Metagenomics, or the analysis of microbial DNA in different environments, has dramatically increased what is known about microbial life. These sequencing-based techniques are not dependent on culturing microbes, which can be an incredibly difficult undertaking. However, isolating and cultivating microbes remains important to both confirm and expand upon those results. Moreover, cultivated microbes could potentially be used as probiotics or biocontrol agents or for industrial purposes. To date, most environmental microbes remain uncultured, but metagenomic data can be leveraged to help researchers isolate and cultivate new ones..."

The rest of the transcript, along with a link to the research itself, is available on the resource itself.

This resource is a video abstract of a research paper created by Research Square on behalf of its authors. It provides a synopsis that's easy to understand, and can be used to introduce the topics it covers to students, researchers, and the general public. The video's transcript is also provided in full, with a portion provided below for preview:

"Plant health is essential for food production, but plants are often affected by pathogens that can threaten plant performance including crop yield. Unfortunately, we can often only predict plant health when pathogens have infected plants and can no longer be controlled – and by then it is too late. To counteract pathogens, farmers often apply extensive amounts of pesticides throughout plant growth. But excessive pesticide use is costly and affects the biodiversity of the surrounding species. A recent study sought to find a way to predict plant health before planting. Researchers investigated different classes of soil microbes throughout the growth of tomato plants. They found that bacterial predators called protists were the best predictors of pathogen dynamics in growing plants..."

The rest of the transcript, along with a link to the research itself, is available on the resource itself.

This resource is a video abstract of a research paper created by Research Square on behalf of its authors. It provides a synopsis that's easy to understand, and can be used to introduce the topics it covers to students, researchers, and the general public. The video's transcript is also provided in full, with a portion provided below for preview:

"The soil microbiome is composed of a complex and diverse fungal community, from plant pathogens that reduce plant performance to mutualistic fungal taxa that provide nutrients to plants. One class of mutualists is arbuscular mycorrhizal fungi (AMF), key providers of phosphorus. Although plant hosts and abiotic parameters are known to affect AMF, it remains unknown how fungivorous predators affect AMF communities. A recent study explored the connections between AMF, fungivorous protists and nematodes, and plant performance. In a 17-year field experiment comparing four manure treatments in a low-fertility red soil, researchers found that manure addition increased AMF biomass along with the density of fungivorous nematodes. More AMF was digested by nematodes in high-manure treatments, and network analysis indicated that predation stimulated AMF biomasses and modified community composition..."

The rest of the transcript, along with a link to the research itself, is available on the resource itself.