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Abstract As the use of artificial intelligence (AI) has grown exponentially across a wide variety of science applications, it has become clear that it is critical to share data and code to facilitate reproducibility and innovation. AMS recently adopted the requirement that all papers include an availability statement. However, there is no requirement to ensure that the data and code are actually freely accessible during and after publication. Studies show that without this requirement, data is openly available in about a third to a half of journal articles. In this work, we surveyed two AMS journals, Artificial Intelligence for the Earth Systems (AIES) and Monthly Weather Review (MWR), and two non-AMS journals. These journals varied in primary topic foci, publisher, and requirement of an availability statement. We examined the extent to which data and code are stated to be available in all four journals, if readers could easily access the data and code, and what common justifications were provided for articles without open data or code. Our analysis found that roughly 75% of all articles that produced data and had an availability statement made at least some of their data openly available. Code was made openly available less frequently in three out of the four journals examined. Access was inhibited to data or code in approximately 15% of availability statement that contained at least one link. Finally, the most common justifications for not making data or code openly available referenced dataset size and restrictions of availability from non-co-author entities. 

This database synthesizes trophic information on dinoflagellate and ciliate taxa, emphasizing their crucial roles in marine food webs. The compiled database serves as a valuable resource for understanding the ecological importance of these protists across the global ocean. The database was built from a collection of ecological information and corresponding taxa derived from available literature including observational, experimental, and field-based studies. A full description of the TMD can be found in the Microbiology Resource Announcements Journal (Jones et al. in press). 

ABSTRACT Phylogenies built from multiple genes have become a common component of evolutionary biology studies. Molecular phylogenomic matrices used to build multi-gene phylogenies can be built from either nucleotide or protein matrices. Nucleotide-based analyses are often more appropriate for addressing phylogenetic questions in evolutionarily shallow timescales (i.e., less than 100 million years) while protein-based analyses are often more appropriate for addressing deep phylogenetic questions. PhyloFisher is a phylogenomic software package written in Python3. The manually curated PhyloFisher database contains 240 protein-coding genes from 304 eukaryotic taxa. Here we presentnucl_matrix_constructor.py, an expansion of the PhyloFisher starting database, and an update to PhyloFisher that maintains DNA sequences. This combination will allow users the ability to easily build nucleotide phylogenomic matrices while retaining the benefits of protein-based pre-processing used to identify contaminants and paralogy. 

In the Great Lakes region, total cold-season snowfall consists of contributions from both lake-effect systems (LES) and non-LES snow events. To enhance understanding of the regional hydroclimatology, this research examined these separate contributions with a focus on the cold seasons (October–March) of 2009/2010, a time period with the number of LES days substantially less than the mean, and 2012/2013, a time period with the number of LES days notably greater than the mean, for the regions surrounding Lakes Erie, Michigan, and Ontario. In general, LES snowfall exhibited a maximum contribution in near-shoreline areas surrounding each lake while non-LES snowfall tended to provide a more widespread distribution throughout the entire study regions with maxima often located in regions of elevated terrain. The percent contribution for LES snowfall to the seasonal snowfall varied spatially near each lake with localized maxima and ranged in magnitudes from 10% to over 70%. Although total LES snowfall amounts tended to be greater during the cold season with the larger number of LES days, the percent of LES snowfall contributing to the total cold-season snowfall was not directly dependent on the number of LES days. The LES snowfall contributions to seasonal totals were found to be generally larger for Lakes Erie and Ontario during the cold season with a greater number of LES days; however, LES contributions were similar or smaller for areas in the vicinity of Lake Michigan during the cold season with a smaller number of LES days. 

Climate change is causing larger wildfires and more extreme precipitation events in many regions. As these ecological disturbances increasingly coincide, they alter lateral fluxes of sediment, organic matter, and nutrients. Here, we report the stream chemistry response of watersheds in a semiarid region of Utah (USA) that were affected by a megafire followed by an extreme precipitation event in October 2018. We analyzed daily to hourly water samples at 10 stream locations from before the storm event until three weeks after its conclusion for suspended sediment, solute and nutrient concentrations, water isotopes, and dissolved organic matter concentration, optical properties, and reactivity. The megafire caused a ~2,000-fold increase in sediment flux and a ~6,000-fold increase in particulate carbon and nitrogen flux over the course of the storm. Unexpectedly, dissolved organic carbon (DOC) concentration was 2.1-fold higher in burned watersheds, despite the decreased organic matter from the fire. DOC from burned watersheds was 1.3-fold more biodegradable and 2.0-fold more photodegradable than in unburned watersheds based on 28-day dark and light incubations. Regardless of burn status, nutrient concentrations were higher in watersheds with greater urban and agricultural land use. Likewise, human land use had a greater effect than megafire on apparent hydrological residence time, with rapid stormwater signals in urban and agricultural areas but a gradual stormwater pulse in areas without direct human influence. These findings highlight how megafires and intense rainfall increase short-term particulate flux and alter organic matter concentration and characteristics. However, in contrast with previous research, which has largely focused on burned-unburned comparisons in pristine watersheds, we found that direct human influence exerted a primary control on nutrient status. Reducing anthropogenic nutrient sources could therefore increase socioecological resilience of surface water networks to changing wildfire regimes. 

Abstract In Arctic catchments, bacterioplankton are dispersed through soils and streams, both of which freeze and thaw/flow in phase, seasonally. To characterize this dispersal and its potential impact on biogeochemistry, we collected bacterioplankton and measured stream physicochemistry during snowmelt and after vegetation senescence across multiple stream orders in alpine, tundra, and tundra‐dominated‐by‐lakes catchments. In all catchments, differences in community composition were associated with seasonal thaw, then attachment status (i.e. free floating or sediment associated), and then stream order. Bacterioplankton taxonomic diversity and richness were elevated in sediment‐associated fractions and in higher‐order reaches during snowmelt. FamiliesChthonomonadaceae,Pyrinomonadaceae, andXiphinematobacteraceaewere abundantly different across seasons, whileFlavobacteriaceaeandMicroscillaceaewere abundantly different between free‐floating and sediment‐associated fractions. Physicochemical data suggested there was high iron (Fe⁺) production (alpine catchment); Fe⁺production and chloride (Cl⁻) removal (tundra catchment); and phosphorus (SRP) removal and ammonium (NH₄⁺) production (lake catchment). In tundra landscapes, these ‘hot spots’ of Fe⁺production and Cl⁻removal accompanied shifts in species richness, while SRP promoted the antecedent community. Our findings suggest that freshet increases bacterial dispersal from headwater catchments to receiving catchments, where bacterioplankton‐mineral relations stabilized communities in free‐flowing reaches, but bacterioplankton‐nutrient relations stabilized those punctuated by lakes.