Rewilding the cityUrban Jungle Ben Wilson Doubleday, 2023. 304 pp.

Urban environments can and should be rich reservoirs of biodiversity.

Multi-year and multi-site effects of recurrent glyphosate applications on the wheat rhizosphere microbiome.

Glyphosate (N-(phosphonomethyl)glycine) is broad-spectrum herbicide that is extensively used worldwide, but its effects on the soil microbiome are inconsistent. To provide a sound scientific basis for herbicide re-review and registration decisions, we conducted a four-year (2013-2016) study in which we consecutively applied glyphosate to a wheat (Triticum aestivum L.)-field pea (Pisum sativum L.)-canola (Brassica napus L.)-wheat crop rotation at five sites in the Canadian prairies. The glyphosate rates were 0, 1, 2, 4 and 8 kg ae ha-1, applied pre-seeding and post-harvest every year. The wheat rhizosphere was sampled in the final year of the study and analysed for microbial biomass C (MBC), the composition and diversity of the microbiome, and activities of ß-glucosidase, N-acetyl-ß-glucosiminidase, acid phosphomonoesterase and arylsulphatase. Glyphosate did not affect MBC, the composition and diversity of prokaryotes and fungi, and the activities of three of the four enzymes measured in the wheat rhizosphere. The one effect of glyphosate was a wave-like response of N-acetyl-ß-glucosaminidase activity with increasing application rates. The experimental sites had much greater effects, driven by soil pH and organic C, on the soil microbiome composition and enzyme activities than glyphosate. Soil pH was positively correlated with the relative abundance of Acidobacteriota but negatively correlated with that of Actinobacteriota and Basidiomycota. Soil organic C was positively correlated with the relative abundances of Proteobacteriota and Verrucomicrobiota, but negatively correlated with the relative abundance of Crenachaeota. The activity of acid phosphomonoesterase declined with increasing relative abundance of Acidobacteriota, but increased with that of Actinobacteriota and Basidiomycota. The activity of N-acetyl-ß-glucosaminidase also increased with increasing relative abundance of Actinobacteriota but decreased with that of Mortierellomycota. ß-glucosidase activity also decreased with increasing relative abundance of Mortierellomycota. The core fungal species observed in at least 90% of the samples were Humicola nigrescens, Gibberella tricincta and Giberella fujikuroi. Therefore, this multi-site study on the Canadian prairies revealed no significant effects of 4-year applications of glyphosate applied at different rates on most soil microbial properties despite differences in the properties among sites. However, it is important to keep evaluating glyphosate effects on the soil microbiome and its functioning because it is the most widely used herbicide worldwide.

Why we do what we doDancing Cockatoos and the Dead Man Test Marlene Zuk Norton, 2022. 352 pp.

From regenerating sea slugs to self-medicating sheep, a biologist probes the origins and evolution of behavior.

Microbial composition differs between production systems and is associated with growth performance and carcass quality in pigs.

BACKGROUND: The role of the microbiome in livestock production has been highlighted in recent research. Currently, little is known about the microbiome's impact across different systems of production in swine, particularly between selection nucleus and commercial populations. In this paper, we investigated fecal microbial composition in nucleus versus commercial systems at different time points. RESULTS: We identified microbial OTUs associated with growth and carcass composition in each of the two populations, as well as the subset common to both. The two systems were represented by individuals with sizeable microbial diversity at weaning. At later times microbial composition varied between commercial and nucleus, with species of the genus Lactobacillus more prominent in the nucleus population. In the commercial populations, OTUs of the genera Lactobacillus and Peptococcus were associated with an increase in both growth rate and fatness. In the nucleus population, members of the genus Succinivibrio were negatively correlated with all growth and carcass traits, while OTUs of the genus Roseburia had a positive association with growth parameters. Lactobacillus and Peptococcus OTUs showed consistent effects for fat deposition and daily gain in both nucleus and commercial populations. Similarly, OTUs of the Blautia genus were positively associated with daily gain and fat deposition. In contrast, an increase in the abundance of the Bacteroides genus was negatively associated with growth performance parameters. CONCLUSIONS: The current study provides a first characterization of microbial communities' value throughout the pork production systems. It also provides information for incorporating microbial composition into the selection process in the quest for affordable and sustainable protein production in swine.

Variation in range size and dispersal capabilities of microbial taxa.

Geographic range size can span orders of magnitude for plant and animal species, with the study of why range sizes vary having preoccupied biogeographers for decades. In contrast, there have been few comparable studies of how range size varies across microbial taxa and what traits may be associated with this variation. We determined the range sizes of 74,134 bacterial and archaeal taxa found in settled dust collected from 1,065 locations across the United States. We found that most microorganisms have small ranges and few have large ranges, a pattern similar to the range size distributions commonly observed for macrobes. However, contrary to expectations, those microbial taxa that were locally abundant did not necessarily have larger range sizes. The observed differences in microbial range sizes were generally predictable from taxonomic identity, phenotypic traits, genomic attributes, and habitat preferences, findings that provide insight into the factors shaping patterns of microbial biogeography.

A global database of ant species abundances.

What forces structure ecological assemblages? A key limitation to general insights about assemblage structure is the availability of data that are collected at a small spatial grain (local assemblages) and a large spatial extent (global coverage). Here, we present published and unpublished data from 51 ,388 ant abundance and occurrence records of more than 2,693 species and 7,953 morphospecies from local assemblages collected at 4,212 locations around the world. Ants were selected because they are diverse and abundant globally, comprise a large fraction of animal biomass in most terrestrial communities, and are key contributors to a range of ecosystem functions. Data were collected between 1949 and 2014, and include, for each geo-referenced sampling site, both the identity of the ants collected and details of sampling design, habitat type, and degree of disturbance. The aim of compiling this data set was to provide comprehensive species abundance data in order to test relationships between assemblage structure and environmental and biogeographic factors. Data were collected using a variety of standardized methods, such as pitfall and Winkler traps, and will be valuable for studies investigating large-scale forces structuring local assemblages. Understanding such relationships is particularly critical under current rates of global change. We encourage authors holding additional data on systematically collected ant assemblages, especially those in dry and cold, and remote areas, to contact us and contribute their data to this growing data set.

The Evolution of Stomach Acidity and Its Relevance to the Human Microbiome.

Gastric acidity is likely a key factor shaping the diversity and composition of microbial communities found in the vertebrate gut. We conducted a systematic review to test the hypothesis that a key role of the vertebrate stomach is to maintain the gut microbial community by filtering out novel microbial taxa before they pass into the intestines. We propose that species feeding either on carrion or on organisms that are close phylogenetic relatives should require the most restrictive filter (measured as high stomach acidity) as protection from foreign microbes. Conversely, species feeding on a lower trophic level or on food that is distantly related to them (e.g. herbivores) should require the least restrictive filter, as the risk of pathogen exposure is lower. Comparisons of stomach acidity across trophic groups in mammal and bird taxa show that scavengers and carnivores have significantly higher stomach acidities compared to herbivores or carnivores feeding on phylogenetically distant prey such as insects or fish. In addition, we find when stomach acidity varies within species either naturally (with age) or in treatments such as bariatric surgery, the effects on gut bacterial pathogens and communities are in line with our hypothesis that the stomach acts as an ecological filter. Together these results highlight the importance of including measurements of gastric pH when investigating gut microbial dynamics within and across species.