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- W2891945583 abstract "Macroecology is the study of the mechanisms underlying general patterns of ecology across scales. A major focus of research within macroecology is understanding biodiversity patterns and their underlying processes. The field of macroecology has been biased towards charismatic macroorganisms (also known as macrobes), and has largely ignored insights and breadth that can be gained by considering microorganisms. We argue that microbial ecology and macroecology are united by common currencies (individuals and species), as well as by comparable challenges of documenting their distributions and abundances. Future directions that would lead to a unified macroecology include: expansion of spatial and temporal scales to encompass the diversity of microbes; synthesis-driven, systematic comparisons of macrobial and microbial macroecological patterns and processes; and support of interdisciplinary approaches in training, publishing, and funding to equitably value macrobial and microbial insights into understanding the rules and exceptions of life. Macroecology is the study of the mechanisms underlying general patterns of ecology across scales. Research in microbial ecology and macroecology have long been detached. Here, we argue that it is time to bridge the gap, as they share a common currency of species and individuals, and a common goal of understanding the causes and consequences of changes in biodiversity. Microbial ecology and macroecology will mutually benefit from a unified research agenda and shared datasets that span the entirety of the biodiversity of life and the geographic expanse of the Earth. Macroecology is the study of the mechanisms underlying general patterns of ecology across scales. Research in microbial ecology and macroecology have long been detached. Here, we argue that it is time to bridge the gap, as they share a common currency of species and individuals, and a common goal of understanding the causes and consequences of changes in biodiversity. Microbial ecology and macroecology will mutually benefit from a unified research agenda and shared datasets that span the entirety of the biodiversity of life and the geographic expanse of the Earth. in microbial ecology, the structural gene that encodes the 16S small subunit of the ribosome. It includes both highly conserved and hypervariable regions, which are used for primer design to capture broad phylogenetic diversity and for assessing phylogenetic divergence, respectively. generally positive relationship between the mean abundance a species attains at individual sites, and the number or proportion of all sampled sites at which it is found. variety of species. Biodiversity can be measured using the currencies of individuals and species. These currencies can be used to estimate biodiversity for local communities, planet Earth, and every scale of spatial observation in between. assessment of how the number of species changes as function of an environmental gradient. practice of defining highly resolved microbial taxonomic units by identical nucleotide sequences of marker genes. Also called amplicon sequence variants, sequence variants, oligotypes, and zero-radius OTUs. alpha diversity metric that considers the relationship between the number of species and the number of individuals within species. concept that, within a microbial community, there are several microbial taxa that are capable of performing the same function in the same conditions, and, presumably, at the same rate. sequencing of taxonomically informative marker genes amplified from individuals. in microbial ecology, a gene that is present in only one copy within a microbial genome and encodes a function necessary for life (typically involved in central metabolism). marker sequence flanked by ribosomal operons that is used to phylogenetically distinguish eukaryotic microorganisms, especially fungi. study of the rules and mechanisms (processes) underpinning general patterns of ecology across scales [2Brown J.H. Macroecology. University of Chicago Press, 1995Google Scholar]. in microbial ecology, genes and their sequences that have been used as a signature of microbial diversity. An example is the 16S rRNA gene for bacteria and archaea and the ITS region for fungi. small container containing organisms and substrate that can be replicated and manipulated in the laboratory. Microbial mesocosms can have natural or artificial substrate, like soil or microbiological medium, respectively, and can be seeded with wild communities from a particular habitat or inoculated with specified cultivable members. It is expected that the influences of captivity away from nature (sometimes called container effects) can be minimized in microbial mesocosms. This is because microbial individuals, and their expected effective ranges for interactions with each other and with their environment, are small relative to the volume of the container. sequencing of taxonomically informative marker genes amplified from an environmental sample that contains mixed populations or communities. General primers that target a conserved nucleotide sequence are used to amplify the signal of marker genes from a mixed microbial community. These sequences are typically multiplexed for sequencing, and then they can be used with databases of known sequences to build phylogeny, assign taxonomy, assess alpha diversity, and create an species-by-sample table (OTU table, as in Figure 1A) for community analysis. sequencing of all nucleic acid extracted from an environmental sample, without targeted amplification. Also known as shotgun metagenome sequencing, this method is commonly applied to microbial communities to assess functional potential by annotating sequences against a database of known functional genes. broadly defined as those organisms too small to be visible with the naked eye, including viruses, bacteria, archaea, protists, a subset of fungi, or even the smallest arthropods (such as face mites). When evolutionarily defined, microorganisms include the domains of bacteria and archaea (previously, prokaryotes), which were the first evolved lineages that through endosymbiosis gave rise to eukarya. species concept that is based on morphology, and is commonly used in the fields of entomology and botany. Unidentifiable individuals with shared physical characteristics are grouped artificially into an operational taxonomic unit without reference to other distinguishing traits. number or proportion of sites in which a species is detected. approximations of species that are commonly used in the field of microbial ecology, arbitrarily defined as informed by the technology used to observe the microorganisms. For example, 16S rRNA gene amplicon sequencing datasets often define OTUs at 97% gene sequence identity. Thus, all sequences that are 97% similar would be counted towards a single OTU. nonsexual mechanisms for transferring genetic material, common among single-celled organisms like bacteria, archaea, protists, and fungi. within a dataset, taxa that are observed only once and in an abundance of one individual. In microbial ecology, this often refers to a singly observed unique sequence of a marker gene. depicts the number of individuals (N) of each species in a sample, and is often expressed as a relationship between the logarithm of N plotted against species rank (from the most to the least abundant species). relates the number of species (S) to the area of the plot (gray squares) in which species richness is sampled (A). In the nested SAR, larger areas should be therefore contiguous and should encompass all the smaller areas. However, empirical SARs are often constructed based on much smaller samples, which are assumed to be representative of the whole contiguous and mutually adjacent areas." @default.
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- W2891945583 date "2018-10-01" @default.
- W2891945583 modified "2023-10-15" @default.
- W2891945583 title "Macroecology to Unite All Life, Large and Small" @default.
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