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Biodiversity loss is one of the main challenges of our time, 1 , 2 and attempts to address it require a clear understanding of how ecological communities respond to environmental change across time and space. 3 , 4 While the increasing availability of global databases on ecological communities has advanced our knowledge of biodiversity sensitivity to environmental changes, 5 , 6 , 7 vast areas of the tropics remain understudied. 8 , 9 , 10 , 11 In the American tropics, Amazonia stands out as the world's most diverse rainforest and the primary source of Neotropical biodiversity, 12 but it remains among the least known forests in America and is often underrepresented in biodiversity databases. 13 , 14 , 15 To worsen this situation, human-induced modifications 16 , 17 may eliminate pieces of the Amazon's biodiversity puzzle before we can use them to understand how ecological communities are responding. To increase generalization and applicability of biodiversity knowledge, 18 , 19 it is thus crucial to reduce biases in ecological research, particularly in regions projected to face the most pronounced environmental changes. We integrate ecological community metadata of 7,694 sampling sites for multiple organism groups in a machine learning model framework to map the research probability across the Brazilian Amazonia, while identifying the region's vulnerability to environmental change. 15%-18% of the most neglected areas in ecological research are expected to experience severe climate or land use changes by 2050. This means that unless we take immediate action, we will not be able to establish their current status, much less monitor how it is changing and what is being lost., Competing Interests: Declaration of interests The authors declare no competing interests., (Copyright © 2023 The Authors. Published by Elsevier Inc. All rights reserved.)

The Neotropical region hosts 4225 freshwater fish species, ranking first among the world's most diverse regions for freshwater fishes. Our NEOTROPICAL FRESHWATER FISHES data set is the first to produce a large-scale Neotropical freshwater fish inventory, covering the entire Neotropical region from Mexico and the Caribbean in the north to the southern limits in Argentina, Paraguay, Chile, and Uruguay. We compiled 185,787 distribution records, with unique georeferenced coordinates, for the 4225 species, represented by occurrence and abundance data. The number of species for the most numerous orders are as follows: Characiformes (1289), Siluriformes (1384), Cichliformes (354), Cyprinodontiformes (245), and Gymnotiformes (135). The most recorded species was the characid Astyanax fasciatus (4696 records). We registered 116,802 distribution records for native species, compared to 1802 distribution records for nonnative species. The main aim of the NEOTROPICAL FRESHWATER FISHES data set was to make these occurrence and abundance data accessible for international researchers to develop ecological and macroecological studies, from local to regional scales, with focal fish species, families, or orders. We anticipate that the NEOTROPICAL FRESHWATER FISHES data set will be valuable for studies on a wide range of ecological processes, such as trophic cascades, fishery pressure, the effects of habitat loss and fragmentation, and the impacts of species invasion and climate change. There are no copyright restrictions on the data, and please cite this data paper when using the data in publications., (© 2022 The Ecological Society of America.)

Large wood plays a critical role providing complex habitat structure in rivers and streams. The instream wood regime consists of wood recruitment, transport, retention, and decay in river corridors. In tropical streams, transport and decay are thought to be the dominant influences on the amount instream wood stored, and these are driven by upstream forest cover, as well as catchment hydroclimatic and geomorphic characteristics. Lack of studies of the tropical wood regime leave many uncertainties. Notably, the wood regimes in the neotropical Amazon and Cerrado biomes are not known, and rapidly changing land-use threatens efforts to understand their natural wood regime. We investigated predictors of instream wood in catchments of the Amazon and Cerrado subject to a wide range of agricultural land use to identify the critical factors controlling wood recruitment and load. Using the structural equation modelling technique, we disentangled the complex net of regional and local controls. Contrary to our expectations, local drivers, such as the relation between the piece size and channel dimensions, discharge, stream power and riparian forest were the most important predictors of instream wood. The amounts of wood found in these streams were primarily the result of the wood delivered by the local riparian forest and how much of that wood remains trapped. Therefore, the preservation of the forested riparian zones in Amazon and Cerrado streams is crucial for maintaining the sources of wood as well as the channel morphology capable of trapping and retaining instream wood. Further research should compare reference and disturbed streams to quantify the influence of anthropogenic activities on instream wood and its primary influences. This information would facilitate assessing the extent of human alteration and developing mitigating measures to arrest or reverse changes that reduce instream wood and degrade aquatic and riparian habitat in neotropical rivers and streams.

Instream wood plays important chemical, physical and ecological functions in aquatic systems, benefiting biota directly and indirectly. However, human activities along river corridors have disrupted wood recruitment and retention, usually leading to reductions in the amount of instream wood. In the tropics, where wood is believed to be more transient, the expansion of agriculture and infrastructure might be reducing instream wood stock even more than in the better studied temperate streams. However, research is needed to augment the small amount of information about wood in different biomes and ecosystems of neotropical streams. Here we present the first extensive assessment of instream wood loads and size distributions in streams of the wet-tropical Amazon and semi-humid-tropical Cerrado (the Brazilian savanna). We also compare neotropical wood stocks with those in temperate streams, first comparing against data from the literature, and then from a comparable dataset from temperate biomes in the USA. Contrary to our expectations, Amazon and Cerrado streams carried similar wood loads, which were lower than the world literature average, but similar to those found in comparable temperate forest and savanna streams in the USA. Our results indicate that the field survey methods and the wood metric adopted are highly important when comparing different datasets. But when properly compared, we found that most of the wood in temperate streams is made-up of a small number of large pieces, whereas wood in neotropical streams is made up of a larger number of small pieces that produce similar total volumes. The character of wood volumes among biomes is linked more to the delivery, transport and decomposition mechanisms than to the total number of pieces. Future studies should further investigate the potential instream wood drivers in neotropical catchments in order to better understand the differences and similarities here detected between biomes and climatic regions., Competing Interests: The authors have declared that no competing interests exist.

Conservation initiatives overwhelmingly focus on terrestrial biodiversity, and little is known about the freshwater cobenefits of terrestrial conservation actions. We sampled more than 1500 terrestrial and freshwater species in the Amazon and simulated conservation for species from both realms. Prioritizations based on terrestrial species yielded on average just 22% of the freshwater benefits achieved through freshwater-focused conservation. However, by using integrated cross-realm planning, freshwater benefits could be increased by up to 600% for a 1% reduction in terrestrial benefits. Where freshwater biodiversity data are unavailable but aquatic connectivity is accounted for, freshwater benefits could still be doubled for negligible losses of terrestrial coverage. Conservation actions are urgently needed to improve the status of freshwater species globally. Our results suggest that such gains can be achieved without compromising terrestrial conservation goals., (Copyright © 2020 The Authors, some rights reserved; exclusive licensee American Association for the Advancement of Science. No claim to original U.S. Government Works.)

Brazil contains the largest volume of freshwater of any nation in the world; however, this essential natural resource is threatened by rapid increases in water consumption and water quality degradation, mainly as a result of anthropogenic pressures. Declining water quality has become an increasingly more significant global concern as economic activities and human populations expand and climate change markedly alters hydrological cycles. Changes in land-use/land-cover (LULC) pattern have been recognized as a major driver of water quality degradation, however different LULC types and intensities affect water quality in different ways. In addition, the relationships between LULC and water quality may differ for different spatial and temporal scales. The increase in deforestation, agricultural expansion, and urban sprawl in Brazil highlights the need for water quality protection to ensure immediate human needs and to maintain the quality of water supplies in the long-term. Thus, this manuscript provides an overview of the relationships between LULC and water quality in Brazil, aiming at understanding the effects of different LULC types on water quality, how spatial and temporal scales contribute to these effects, and how such knowledge can improve watershed management and future projections. In general, agriculture and urban areas are the main LULCs responsible for water quality degradation in Brazil. However, although representing a small percentage of the territory, mining has a high impact on water quality. Water quality variables respond differently at different spatial scales, so spatial extent is an important aspect to be considered in studies and management. LULC impacts on water quality also vary seasonally and lag effects mean they take time to occur. Forest restoration can improve water quality and multicriteria evaluation has been applied to identify priority areas for forest restoration and conservation aiming at protecting water quality, but both need further exploration. Watershed modelling has been applied to simulate future impacts of LULC change on water quality, but data availability must be improved to increase the number, locations and duration of studies. Because of the international nature of watersheds and the consistent relationships between land use and water quality in Brazil, we believe our results will also aid water management in other countries., Competing Interests: Declaration of competing interest The authors declare that they have no known competing financial interests or personal relationships that could have appeared to influence the work reported in this paper., (Copyright © 2020 Elsevier Ltd. All rights reserved.)

Agricultural expansion and intensification are major threats to tropical biodiversity. In addition to the direct removal of native vegetation, agricultural expansion often elicits other human-induced disturbances, many of which are poorly addressed by existing environmental legislation and conservation programmes. This is particularly true for tropical freshwater systems, where there is considerable uncertainty about whether a legislative focus on protecting riparian vegetation is sufficient to conserve stream fauna.To assess the extent to which stream fish are being effectively conserved in agricultural landscapes, we examined the spatial distribution of assemblages in river basins to identify the relative importance of human impacts at instream, riparian and catchment scales, in shaping observed patterns. We used an extensive dataset on the ecological condition of 83 low-order streams distributed in three river basins in the eastern Brazilian Amazon.We collected and identified 24,420 individual fish from 134 species. Multiplicative diversity partitioning revealed high levels of compositional dissimilarity (DS) among stream sites (DS = 0.74 to 0.83) and river basins (DS = 0.82), due mainly to turnover (77.8% to 81.8%) rather than nestedness. The highly heterogeneous fish faunas in small Amazonian streams underscore the vital importance of enacting measures to protect forests on private lands outside of public protected areas.Instream habitat features explained more variability in fish assemblages (15%-19%) than riparian (2%-12%), catchment (4%-13%) or natural covariates (4%-11%). Although grouping species into functional guilds allowed us to explain up to 31% of their abundance (i.e. for nektonic herbivores), individual riparian - and catchment - scale predictor variables that are commonly a focus of environmental legislation explained very little of the observed variation (partial R2 values mostly <5%). Policy implications . Current rates of agricultural intensification and mechanization in tropical landscapes are unprecedented, yet the existing legislative frameworks focusing on protecting riparian vegetation seem insufficient to conserve stream environments and their fish assemblages. To safeguard the species-rich freshwater biota of small Amazonian streams, conservation actions must shift towards managing whole basins and drainage networks, as well as agricultural practices in already-cleared land.

Agricultural land use is a primary driver of environmental impacts on streams. However, the causal processes that shape these impacts operate through multiple pathways and at several spatial scales. This complexity undermines the development of more effective management approaches, and illustrates the need for more in-depth studies to assess the mechanisms that determine changes in stream biodiversity. Here we present results of the most comprehensive multi-scale assessment of the biological condition of streams in the Amazon to date, examining functional responses of fish assemblages to land use. We sampled fish assemblages from two large human-modified regions, and characterized stream conditions by physical habitat attributes and key landscape-change variables, including density of road crossings (i.e. riverscape fragmentation), deforestation, and agricultural intensification. Fish species were functionally characterized using ecomorphological traits describing feeding, locomotion, and habitat preferences, and these traits were used to derive indices that quantitatively describe the functional structure of the assemblages. Using structural equation modeling, we disentangled multiple drivers operating at different spatial scales, identifying causal pathways that significantly affect stream condition and the structure of the fish assemblages. Deforestation at catchment and riparian network scales altered the channel morphology and the stream bottom structure, changing the functional identity of assemblages. Local deforestation reduced the functional evenness of assemblages (i.e. increased dominance of specific trait combinations) mediated by expansion of aquatic vegetation cover. Riverscape fragmentation reduced functional richness, evenness and divergence, suggesting a trend toward functional homogenization and a reduced range of ecological niches within assemblages following the loss of regional connectivity. These results underscore the often-unrecognized importance of different land use changes, each of which can have marked effects on stream biodiversity. We draw on the relationships observed herein to suggest priorities for the improved management of stream systems in the multiple-use landscapes that predominate in human-modified tropical forests.

Non-diphtheriae Corynebacterium species have been increasingly recognized as the causative agents of infections in humans. Differential identification of these bacteria in the clinical microbiology laboratory by the most commonly used biochemical tests is challenging, and normally requires additional molecular methods. Herein, we present the annotated draft genome sequences of two isolates of "difficult-to-identify" human-pathogenic corynebacterial species: C. xerosis and C. minutissimum. The genome sequences of ca. 2.7 Mbp, with a mean number of 2,580 protein encoding genes, were also compared with the publicly available genome sequences of strains of C. amycolatum and C. striatum. These results will aid the exploration of novel biochemical reactions to improve existing identification tests as well as the development of more accurate molecular identification methods through detection of species-specific target genes for isolate's identification or drug susceptibility profiling.