Trachydoras is a genus of Doradidae (thorny catfishes) with five nominal valid species distributed in lowland areas of the Amazon, Orinoco, Paraná-Paraguay and Essequibo river basins of South America. A sixth species is described here as Trachydoras gepharti and diagnosed by five characteristics unique among congeners: mental barbels thick, tapered and profusely ornamented with many elongate fleshy papillae loosely arranged in 2–3 rows (vs. mental barbels thinner, papillae lacking or fewer, arranged in 1–2 rows); distinct columns of small, soft papillae along medial and lateral margins of gill filaments on all gill arches (vs. gill filaments lacking conspicuous papillae in congeners); gas bladder acorn-shaped (vs. cordiform) with smooth anterolateral shoulder (vs. shoulder with accessory diverticulum) and terminal diverticula medially united into singular, finger-like projection formed mostly by elongation of only one of the two posterior chambers (vs. both chambers elongated, contributing more or less equally to terminal diverticula in congeners or terminal diverticula absent or reduced in some specimens of T. nattereri and T. paraguayensis). Trachydoras gepharti is known from the Amazon and Orinoco basins where it often occurs syntopically with T. microstomus, T. nattereri and a separate undescribed species of Trachydoras. Like other species of Trachydoras, T. gepharti is specialized for vacuuming chironomid larvae from sandy substrates in medium to large river channels. Redescriptions and diagnoses are provided for the five nominal valid species of Trachydoras along with a key to identification and comments on characteristics used to diagnose the genus and delimit species. Designations include a lectotype (NMW 46375, 91.7 mm SL) for Trachydoras brevis (Kner 1853) and neotype (ANSP 178443, 100 mm SL) for T. nattereri (Steindachner 1881). The true holotype of T. microstomus (Eigenmann 1912) is identified as FMNH 118302 [ex. FMNH 53207, ex. CM 1650] and the specimen previously cataloged as the holotype (FMNH 53206) is identified as T. brevis.

A new species of Hyphessobrycon is described from the middle and lower rio Xingu Basin, Pará state, Brazil. The new species can be distinguished from all congeners by the combination of a large caudal peduncle blotch (largest in mature males), absence of humeral blotch, and largest teeth on dentary, inner premaxillary and maxillary relatively compressed with 6–9 cusps. The new species is compared to three other congeners with similar color pattern: Hyphessobrycon diastatosDagosta, Marinho & Camelier 2014, Hy. negodaguaLima & Gerhard 2001, and Hy. parvellus Ellis 1911, and one species of Hemigrammus, He. rodwayi Durbin 1909.

Crenicichla dandara, new species, is endemic to the rio Xingu above the Belo Monte narrows, and its major left bank tributary the rio Iriri. The new species is distinguished from all congeners by the following combination of characters: body uniformly black (live fishes) or dark brown (preserved specimens) in adults and 74–86 scales in the E1 row. Crenicichla dandara is considered herein to be the tenth species of the C. lugubris group, but its allies within the group are not clear. Among members of this group, C. dandara is most similar in general body shape, snout characteristics and squamation to C. lugubris and C. adspersa, but lacks a caudal-fin blotch as does C. johanna and C. monicae, a condition rare within the Crenicichla-Teleocichla clade. The overall black coloration in Crenicichla dandara is shared with the syntopic, but not closely related, Teleocichla preta. Both species inhabit clear water rapids where they hide among the shadows of large rocks, suggesting that the dark coloration is for camouflage and ambush predation. Based on a preliminary assessment of its conservation status following the criteria and categories of IUCN classification, Crenicichla dandara is considered as a species of least concern (LC).

Results are presented on species richness and distribution of the crustacean fauna obtained by iXingu Project expeditions along the middle and lower Xingu River during low and high water seasons primarily from 2013–2014, prior to the completion of the Belo Monte dam complex. The checklist includes the parasitic and decapod crustacean species surveyed in the Xingu River from the mouth of its tributary, the Iriri River, to its confluence with the Amazon River. With the addition of records from the scientific literature, a total of 32 species representing 18 genera in eight families are known to occur in the middle to lower Xingu basin: four species of fish lice, family Argulidae, four parasitic isopods, families Corallanidae (1 species) and Cymothoidae (3), 13 decapod crabs, families Pseudothelphusidae (5) and Trichodactylidae (8), and 11 decapod shrimps, families Sergestidae (1), Euryrhynchidae (3), and Palaemonidae (7). Seventeen species are recorded for the first time from the Xingu basin, highlighting the importance of focused sampling of decapods and other crustaceans in major sub-basins of the Amazon. The lower Xingu, below the Volta Grande rapids, held the most diversity with 19 species. The Volta Grande rapids (between Altamira and the lower Xingu) and the middle Xingu above Altamira exhibited 17 and 15 species, respectively. Based on comparisons to other Amazon and South American river basins, the middle and lower Xingu River supports a remarkably high diversity of decapods.

A new species of Platydoras is described from the rio Xingu Basin, Brazil. Platydoras birindellii is distinguished from congeners by having gas bladder simple (vs. with posterior secondary chamber) and dorsal and caudal fins uniformly dusky (vs. with distinct marks composed of dark broad band or blotch on central portion of dorsal fin and pair of dark broad stripes on caudal fin, one central to each lobe). Platydoras birindellii shares a simple gas bladder with the sister taxon to Platydoras,Centrochir crocodili, a monotypic genus endemic to the Magdalena Basin. With respect to the caudal skeleton, the parhypural is incompletely fused to hypurals 1+2 in P. birindellii, a condition that is intermediate between those of Centrochir (parhypural typically separated from hypurals 1+2 by distinct suture) and Platydoras (parhypural typically fully fused to hypurals 1+2). Platydoras birindellii is commonly found in rocky clearwater rapids and apparently endemic to the middle and upper portions of the Xingu draining the Brazilian Shield.

Rheodreissena Geda et al. 2018, a recently described genus of Dreissenidae, is represented by living species that inhabit inland freshwaters of Brazil and Venezuela. The type species of Rheodreissena is R. hoeblichi (Schütt 1991a) described from the lower Orinoco basin, Venezuela. Three species are added in this study: R. lopesi (Alvarenga & Ricci, 1989) from the Tocantins and Xingu basins; R. cordilineata n. sp. from the Madeira, Trombetas and Xingu basins, and R. xinguana n. sp. from the Tapajós and Xingu basins. Those three species are recorded from Volta Grande, the stretch of the Xingu River impacted by the Belo Monte dam complex. All Rheodreissena typically attach in shallow clusters to clean, rocky substrates associated with rapids in the main channels of large clear water rivers. Species of Rheodreissena are distinguished by aspects of shell morphology and soft anatomy that presumably reflect adaptations to a rheophilic lifestyle.

During a pilot survey, sponges and mollusks were sampled from the bottom of the middle Xingu River (rapids) and lower Xingu River (ria) via hand-picking in shallows and trawling and surface-supplied dives in deeper waters. The survey revealed a benthic community composed of eight sponge species in four genera and three families, and added six species to the Xingu Basin fauna. Sponges exhibited distinct variation in body shape corresponding to local environmental conditions such as water depth, current velocity and available substrates. Sponges inhabiting rocky bottoms in swift currents (rapids) typically formed crusts. Those in the deeper, calmer waters of the ria attained massive and elaborate forms while attached to infaunal bivalves. Oncosclera navicella and Drulia cristata exhibited crusts and massive forms as adaptations to rapids and ria, respectively. In the middle to lower Xingu, sponges encrusted the shells of eleven species of bivalves (seven infaunal, three epifaunal, and one infaunal/epifaunal) and one infaunal/epifaunal gastropod. Bivalves provide key substrates for supporting sponges above the sand, mud and detritus of the Xingu ria. Potential impacts of the Belo Monte Dam complex on the sponge fauna of the middle Xingu rapids are discussed.

A new species of Creagrutus is described from the upper rio Xingu basin, Mato Grosso state, Brazil. The new species can be distinguished from its congeners by a combination of characters that includes dorsal fin mostly black, a dark oblique blotch on middle and upper-inferior caudal-fin rays, and presence of only two rows of premaxillary teeth. Creagrutus mucipu, formerly known only from the upper rio Tocantins basin in Brazil, is recorded herein as occurring syntopically with the new species in the upper rio Xingu basin.

A new species of Bryconops is described from the rio Xingu Basin, Brazil, that differs from all congeners by the following combination of characters: predorsal scales 8–9, perforated scales in the lateral line 43–45, and pigmentation pattern composed of wide silvery midlateral band on body, hyaline dorsal and anal fins (in alcohol), and dark blotch on distal half of dorsal caudal-fin lobe. The new species shares with members of the subgenus Bryconops maxillary relatively short, edentulous or with one conical tooth, and gill rakers without ossified denticles. The middle and lower Xingu support a remarkable diversity of Bryconops composed of at least nine species-level taxa; comments on their local distributions and habitats are provided, as well as a key to their identification.

Herbivorous fishes feed on stems, leaves, flowers, seeds, fruits, and nuts of diverse aquatic plants, as well as algae. Pacus are the herbivorous cousins of piranhas and consume a myriad of diets comprised of these plant products, but a few species are phytophages, herbivores that feed almost exclusively on rapids-dwelling (rheophilic) riverweed plants from the family Podostemaceae. The degree to which pacus feed on riverweed varies from obligate year-round consumption to strictly seasonal, facultative feeding. Obligate phytophages feed heavily on riverweed and strictly occur in river rapids, while facultative phytophages only consume riverweed during seasons with low flow. Does ecological specialization (diet) beget morphological specialization in the feeding apparatus and/or body shape of phytophages? Under a phylogenetic framework, we used micro-computed tomography (µCT) scanning to compare functional feeding traits among 26 species of serrasalmids, four of which are obligate phytophages. We also compared body shape between pacus using geometric morphometrics to identify potential locomotor adaptations for rheophily. Obligate phytophages have dentitions and slicing jaws well-suited for shearing fleshy plant material relative to other pacus, which are equipped with fruit and seed crushing morphologies. Unrelated obligate phytophages have also converged on a similar body shape that is distinct from sympatric congeneric herbivores. Phytophagy involves more consistent changes to body shape than to feeding morphology, suggesting that body shape has more important ties to diet.

We discuss new applications of baited remote underwater video (BRUV) systems based on recordings of Amazonian freshwater fauna during a long-term fish monitoring program in the Xingu River, Brazil. BRUVs facilitated estimates of relative abundance and frequency of occurrence for species of river turtles (Podocnemis unifilis, P. expansa, Rhinoclemmys punctularia), river dolphin (Inia geoffrensis) and spectacled caiman (Caiman crocodilus) in a variety of habitats including rocky rapids, submerged sandy beaches, an artificial reservoir and the Xingu Ria.

Remote sensing is an invaluable tool to objectively illustrate the rapid decline in habitat extents worldwide. The many operational Earth Observation platforms provide options for the generation of land cover maps, each with unique characteristics and considerable semantic differences in the definition of classes. As a result, differences in baseline estimates are inevitable. Here we compare forest cover and surface water estimates over four time periods spanning three decades (1989–2018) for ∼1.3 million km² encompassing the Xingu River Basin, Brazil, from published, freely accessible remotely sensed land cover classifications. While all showed a decrease in forest extent over time, the total deforested area reported by each ranged widely for all time periods. The greatest differences ranged from 9% to 17% (116,958 to 219,778 km²) deforestation of the total area for year 2000 and 2014–2018 time period, respectively. We also show the high sensitivity of forest fragmentation metrics (entropy and foreground area density) to data quality and spatial resolution, with cloud cover and sensor artefacts resulting in errors. Surface water classifications must be chosen carefully because sources differ greatly in location and mapped area of surface water. After operationalization of the Belo Monte dam complex, the large reservoirs are notably absent from several of the classifications illustrating land cover. Freshwater ecosystem health is influenced by the land cover surrounding water bodies (e.g., riparian zones). Understanding differences between the many remotely sensed baselines is fundamentally important to avoid information misuse, and to objectively choose the most appropriate classification for ecological studies, conservation, or policy making. The differences between the classifications examined here are not a failure of the technology, but due to different interpretations of ‘forest cover’ and characteristics of the input data (e.g., spatial resolution). Our findings demonstrate the importance of transparency in the generation of remotely sensed classifications and the need for users to familiarize themselves with the characteristics and limitations of each data set.

Synbranchus (swamp eel) specimens exhibiting remarkable variation were collected from different habitats during recent fieldwork in the Xingu Basin, Brazil. For this study, those specimens were first sorted into about six morphotypes based on external morphology, especially color pattern. Representatives of each morphotype and additional specimens extralimital to the Xingu Basin were then sequenced for three mitochondrial genes (ATPase 8/6, 16s, and Cytb) and one nuclear (Rag1). Molecular phylogenetic analyses using Maximum Parsimony and Bayesian methods supported the recognition of five distinct lineages of Synbranchus in the middle to lower Xingu Basin and up to 10 species-level lineages across all samples. Two of the Xingu lineages were subsequently identified as the nominal S. marmoratus and S. madeirae, and another two were provisionally treated as Synbranchus spp. 5 and 7. The fifth lineage is formally described here as Synbranchus royal, distinguished by its extremely pronounced nuchal hump with dorsal head profile distinctly concave and rising steeply from above middle of eye vs. nuchal region moderately bulbous with dorsal profile ascending more gradually, straight or with shallow concavity behind eye (S. marmoratus) or nuchal hump lacking, dorsal profile ascending modestly, straight to scarcely concave behind eye (S. lampreia and S. madeirae); and relatively deep body, maximum depth at middle of TL 4.7–5.4% TL (vs. 3.2–4.8% TL in congeners). Synbranchus royal and Synbranchus sp. 7 were found in rocky rapids of main channels of the middle Xingu on the Brazilian Shield uplands, a sharp departure from the lentic habitats commonly associated with synbranchid (swamp) eels.

Variation in water quality affects species distributions and community structure within Amazonian rivers. Documentation of physical, chemical, or biological characteristics is an important step towards understanding the ecological interactions in these rivers, especially in advance of acute and long-term changes. The goal of this study was to help establish baseline conditions in the Xingu River prior to the operation of a large run-of-the-river dam complex, Belo Monte. The Middle Xingu River is a mixed bedrock-alluvial anabranching system with annual low-water (September–October) and high-water (March–April) periods. Based on 1969–2014 discharge data for the Middle Xingu, the annual difference between the highest and lowest flow rates averaged 22,034 m³/s and varied from 12,464 m³/s (1998) to 31,681 m³/s (1980), resulting in annual differences in water levels from 3.39 m to 6.34 m (avg. 4.88 m). Hydrograms proposed by the dam engineers severely attenuate the Xingu's flood pulse, permitting only 19.5 or 30.4% of the river's average annual flow into the 100 km stretch below the diversion (in-stream) dam and above the outflow of the main (off-stream) dam. Proposals to increase the amount of water released into the dewatered stretch (e.g., Hidrograma Piracema) are still below the average of minimum flow rates for seven months out of the year, including the four months spanning the annual flood pulse.

Physicochemical variables measured in the Middle to Lower Xingu mainstem revealed differences between hydrological periods (low, high, and rising waters), with sites primarily differentiated by temporal differences in temperature, dissolved oxygen, and water clarity. pH values reported from the Xingu mainstem rank among the highest (most alkaline) recorded for major Neotropical rivers, with averages of 7.6, 7.3 and 7.9 for the low-, high- and rising-water periods, respectively. Water temperature, pH, and nutrient concentrations were greater than previously reported for the Middle to Lower Xingu River, suggesting that changes in the Upper Xingu Basin associated with increased agricultural development also may be occurring downstream. Xingu water transparency and conductivity were typical of a clearwater river. Physicochemical parameters showed more variation (extreme values) among tributaries and floodplain habitats, and often differed from those nearby in the Xingu mainstem. Benthic chlorophyll-a concentrations collected after a 21-day deployment of experimental tiles varied widely, with an average of 29.88 ± 27.25 mg/m² during the low-water period. Leaf litter breakdown rates in the Xingu were intermediate, with a mean processing coefficient of 0.010 ± 0.001. The potential synergistic effects of multiple stressors make continued monitoring of water quality and biota critical, and highlight the need for studies exploring the physiological tolerances of species of conservation concern to develop robust strategies for preserving the Xingu River's unique biodiversity.