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Climate-driven changes in freshwater inputs have been shown to affect the structure and function of coastal ecosystems. We evaluated changes in the influence of river runoff on coastal systems of Northwestern Patagonia (NWP) over recent decades (1993-2021) by combined analysis of long-term streamflow time series, hydrological simulation, satellite-derived and reanalysis data on sea surface conditions (temperature, turbidity, and salinity). Significant decreases in minimum streamflow across a zone spanning six major river basins were evident at weekly, monthly, and seasonal scales. These changes have been most pronounced in mixed-regime northern basins (e.g., Puelo River) but appear to be progressing southward to rivers characterised by a nival regime. In the adjacent two-layer inner sea, reduced freshwater input corresponds with a shallower halocline and increased surface temperatures across northern Patagonia. Our results underscore the rapidly evolving influence of rivers on adjacent estuarine and coastal waters in NWP. We highlight the need for cross-ecosystem observation, forecasting, mitigation and adaptation strategies in a changing climate, together with corresponding adaptive basin management of systems that supply runoff to the coastal marine waters.

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Microbes in marine ecosystems have evolved their gene content to thrive successfully in the cold. Although this process has been reasonably well studied in bacteria and selected eukaryotes, less is known about the impact of cold environments on the genomes of viruses that infect eukaryotes. Here, we analyzed cold adaptations in giant viruses (Nucleocytoviricota and Mirusviricota) from austral marine environments and compared them with their Arctic and temperate counterparts. We recovered giant virus metagenome-assembled genomes (98 Nucleocytoviricota and 12 Mirusviricota MAGs) from 61 newly sequenced metagenomes and metaviromes from sub-Antarctic Patagonian fjords and Antarctic seawater samples. When analyzing our data set alongside Antarctic and Arctic giant viruses MAGs already deposited in the Global Ocean Eukaryotic Viral database, we found that Antarctic and Arctic giant viruses predominantly inhabit sub-10°C environments, featuring a high proportion of unique phylotypes in each ecosystem. In contrast, giant viruses in Patagonian fjords were subject to broader temperature ranges and showed a lower degree of endemicity. However, despite differences in their distribution, giant viruses inhabiting low-temperature marine ecosystems evolved genomic cold-adaptation strategies that led to changes in genetic functions and amino acid frequencies that ultimately affect both gene content and protein structure. Such changes seem to be absent in their mesophilic counterparts. The uniqueness of these cold-adapted marine giant viruses may now be threatened by climate change, leading to a potential reduction in their biodiversity.

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Indigenous societies are known to have occupied the Amazon basin for more than 12,000 years, but the scale of their influence on Amazonian forests remains uncertain. We report the discovery, using LIDAR (light detection and ranging) information from across the basin, of 24 previously undetected pre-Columbian earthworks beneath the forest canopy. Modeled distribution and abundance of large-scale archaeological sites across Amazonia suggest that between 10,272 and 23,648 sites remain to be discovered and that most will be found in the southwest. We also identified 53 domesticated tree species significantly associated with earthwork occurrence probability, likely suggesting past management practices. Closed-canopy forests across Amazonia are likely to contain thousands of undiscovered archaeological sites around which pre-Columbian societies actively modified forests, a discovery that opens opportunities for better understanding the magnitude of ancient human influence on Amazonia and its current state.

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[This corrects the article DOI: 10.3389/fmicb.2022.862812.].

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Archaeological remains of agrarian-based, low-density urbananism1-3 have been reported to exist beneath the tropical forests of Southeast Asia, Sri Lanka and Central America4-6. However, beyond some large interconnected settlements in southern Amazonia7-9, there has been no such evidence for pre-Hispanic Amazonia. Here we present lidar data of sites belonging to the Casarabe culture (around AD 500 to AD 1400)10-13 in the Llanos de Mojos savannah-forest mosaic, southwest Amazonia, revealing the presence of two remarkably large sites (147 ha and 315 ha) in a dense four-tiered settlement system. The Casarabe culture area, as far as known today, spans approximately 4,500 km2, with one of the large settlement sites controlling an area of approximately 500 km2. The civic-ceremonial architecture of these large settlement sites includes stepped platforms, on top of which lie U-shaped structures, rectangular platform mounds and conical pyramids (which are up to 22 m tall). The large settlement sites are surrounded by ranked concentric polygonal banks and represent central nodes that are connected to lower-ranked sites by straight, raised causeways that stretch over several kilometres. Massive water-management infrastructure, composed of canals and reservoirs, complete the settlement system in an anthropogenically modified landscape. Our results indicate that the Casarabe-culture settlement pattern represents a type of tropical low-density urbanism that has not previously been described in Amazonia.

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The activity of marine microorganisms depends on community composition, yet, in some oceans, less is known about the environmental and ecological processes that structure their distribution. The objective of this study was to test the effect of geographical distance and environmental parameters on prokaryotic community structure in the Southern Ocean (SO). We described the total (16S rRNA gene) and the active fraction (16S rRNA-based) of surface microbial communities over a ~6,500 km longitudinal transect in the SO. We found that the community composition of the total fraction was different from the active fraction across the zones investigated. In addition, higher α-diversity and stronger species turnover were displayed in the active community compared to the total community. Oceanospirillales, Alteromonadales, Rhodobacterales, and Flavobacteriales dominated the composition of the bacterioplankton communities; however, there were marked differences at the order level. Temperature, salinity, silicic acid, particulate organic nitrogen, and particulate organic carbon correlated with the composition of bacterioplankton communities. A strong distance-decay pattern between closer and distant communities was observed. We hypothesize that it was related to the different oceanic fronts present in the Antarctic Circumpolar Current. Our findings contribute to a better understanding of the complex arrangement that shapes the structure of bacterioplankton communities in the SO.

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The southwestern Amazon Rainforest Ecotone (ARE) is the transitional landscape between the tropical forest and seasonally flooded savannahs of the Bolivian Llanos de Moxos. These heterogeneous landscapes harbour high levels of biodiversity and some of the earliest records of human occupation and plant domestication in Amazonia. While persistent Indigenous legacies have been demonstrated elsewhere in the Amazon, it is unclear how past human-environment interactions may have shaped vegetation composition and structure in the ARE. Here, we examine 6000 years of archaeological and palaeoecological data from Laguna Versalles (LV), Bolivia. LV was dominated by stable rainforest vegetation throughout the Holocene. Maize cultivation and cultural burning are present after ca 5700 cal yr BP. Polyculture cultivation of maize, manioc and leren after ca 3400 cal yr BP predates the formation of Amazonian Dark/Brown Earth (ADE/ABE) soils (approx. 2400 cal yr BP). ADE/ABE formation is associated with agroforestry indicated by increased edible palms, including Mauritia flexuosa and Attalea sp., and record levels of burning, suggesting that fire played an important role in agroforestry practices. The frequent use of fire altered ADE/ABD forest composition and structure by controlling ignitions, decreasing fuel loads and increasing the abundance of plants preferred by humans. Cultural burning and polyculture agroforestry provided a stable subsistence strategy that persisted despite pronounced climate change and cultural transformations and has an enduring legacy in ADE/ABE forests in the ARE. This article is part of the theme issue 'Tropical forests in the deep human past'.

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Megafauna paintings have accompanied the earliest archaeological contexts across the continents, revealing a fundamental inter-relationship between early humans and megafauna during the global human expansion as unfamiliar landscapes were humanized and identities built into new territories. However, the identification of extinct megafauna from rock art is controversial. Here, we examine potential megafauna depictions in the rock art of Serranía de la Lindosa, Colombian Amazon, that includes a giant sloth, a gomphothere, a camelid, horses and three-toed ungulates with trunks. We argue that they are Ice Age rock art based on the (i) naturalistic appearance and diagnostic morphological features of the animal images, (ii) late Pleistocene archaeological dates from La Lindosa confirming the contemporaneity of humans and megafauna, (iii) recovery of ochre pigments in late Pleistocene archaeological strata, (iv) the presence of most megafauna identified in the region during the late Pleistocene as attested by archaeological and palaeontological records, and (v) widespread depiction of extinct megafauna in rock art across the Americas. Our findings contribute to the emerging picture of considerable geographical and stylistic variation of geometric and figurative rock art from early human occupations across South America. Lastly, we discuss the implications of our findings for understanding the early human history of tropical South America. This article is part of the theme issue 'Tropical forests in the deep human past'.

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The onset of plant cultivation is one of the most important cultural transitions in human history1-4. Southwestern Amazonia has previously been proposed as an early centre of plant domestication, on the basis of molecular markers that show genetic similarities between domesticated plants and wild relatives4-6. However, the nature of the early human occupation of southwestern Amazonia, and the history of plant cultivation in this region, are poorly understood. Here we document the cultivation of squash (Cucurbita sp.) at about 10,250 calibrated years before present (cal. yr BP), manioc (Manihot sp.) at about 10,350 cal. yr BP and maize (Zea mays) at about 6,850 cal. yr BP, in the Llanos de Moxos (Bolivia). We show that, starting at around 10,850 cal. yr BP, inhabitants of this region began to create a landscape that ultimately comprised approximately 4,700 artificial forest islands within a treeless, seasonally flooded savannah. Our results confirm that the Llanos de Moxos is a hotspot for early plant cultivation and demonstrate that-ever since their arrival in Amazonia-humans have markedly altered the landscape, with lasting repercussions for habitat heterogeneity and species conservation.

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The long-term response of ancient societies to climate change has been a matter of global debate. Until recently, the lack of integrative studies using archaeological, palaeoecological and palaeoclimatological data prevented an evaluation of the relationship between climate change, distinct subsistence strategies and cultural transformations across the largest rainforest of the world, Amazonia. Here we review the most relevant cultural changes seen in the archaeological record of six different regions within Greater Amazonia during late pre-Columbian times. We compare the chronology of those cultural transitions with high-resolution regional palaeoclimate proxies, showing that, while some societies faced major reorganization during periods of climate change, others were unaffected and even flourished. We propose that societies with intensive, specialized land-use systems were vulnerable to transient climate change. In contrast, land-use systems that relied primarily on polyculture agroforestry, resulting in the formation of enriched forests and fertile Amazonian dark earth in the long term, were more resilient to climate change.

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Here, we present the interannual distribution of Dinophysis acuminata and Protoceratium reticulatum over a 10-year period in the Reloncaví Fjord, a highly stratified fjord in southern Chile. A realized subniche approach based on the Within Outlying Mean Index (WitOMI) was used to decompose the species' realized niche into realized subniches (found within subsets of environmental conditions). The interannual distribution of both D. acuminata and P. reticulatum summer blooms was strongly influenced by climatological regional events, i.e., El Niño Southern Oscillation (ENSO) and the Southern Annual Mode (SAM). The two species showed distinct niche preferences, with blooms of D. acuminata occurring under La Niña conditions (cold years) and low river streamflow whereas P. reticulatum blooms were observed in years of El Niño conditions and positive SAM phase. The biological constraint exerted on the species was further estimated based on the difference between the existing fundamental subniche and the realized subniche. The observed patterns suggested that D. acuminata was subject to strong biological constraint during the studied period, probably as a result of low cell densities of its putative prey (the mixotrophic ciliate Mesodinium cf. rubrum) usually observed in the studied area.

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The South American Monsoon System is responsible for the majority of precipitation in the continent, especially over the Amazon and the tropical savannah, known as 'Cerrado'. Compared to the extensively studied subtropical and temperate regions the effect of the Medieval Climate Anomaly (MCA) on the precipitation over the tropics is still poorly understood. Here, we present a multiproxy paleoprecipitation reconstruction showing a consistent change in the hydrologic regime during the MCA in the eastern Amazon and 'Cerrado', characterized by a substantial transition from humid to drier conditions during the Early (925-1150 C.E.) to Late-MCA (1150-1350 C.E.). We compare the timing of major changes in the monsoon precipitation with the expansion and abandonment of settlements reported in the archeological record. Our results show that important cultural successions in the pre-Columbian Central Amazon, the transition from Paredão to Guarita phase, are in agreement with major changes in the hydrologic regime. Phases of expansion and, subsequent abandonment, of large settlements from Paredão during the Early to Late-MCA are coherent with a reduction in water supply. In this context we argue that the sustained drier conditions during the latter period may have triggered territorial disputes with Guarita leading to the Paredão demise.

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The legacy of pre-Columbian land use in the Amazonian rainforest is one of the most controversial topics in the social1-10 and natural sciences11,12. Until now, the debate has been limited to discipline-specific studies, based purely on archaeological data8, modern vegetation13, modern ethnographic data3 or a limited integration of archaeological and palaeoecological data12. The lack of integrated studies to connect past land use with modern vegetation has left questions about the legacy of pre-Columbian land use on the modern vegetation composition in the Amazon, unanswered11. Here, we show that persistent anthropogenic landscapes for the past 4,500 years have had an enduring legacy on the hyperdominance of edible plants in modern forests in the eastern Amazon. We found an abrupt enrichment of edible plant species in fossil lake and terrestrial records associated with pre-Columbian occupation. Our results demonstrate that, through closed-canopy forest enrichment, limited clearing for crop cultivation and low-severity fire management, long-term food security was attained despite climate and social changes. Our results suggest that, in the eastern Amazon, the subsistence basis for the development of complex societies began ~4,500 years ago with the adoption of polyculture agroforestry, combining the cultivation of multiple annual crops with the progressive enrichment of edible forest species and the exploitation of aquatic resources. This subsistence strategy intensified with the later development of Amazonian dark earths, enabling the expansion of maize cultivation to the Belterra Plateau, providing a food production system that sustained growing human populations in the eastern Amazon. Furthermore, these millennial-scale polyculture agroforestry systems have an enduring legacy on the hyperdominance of edible plants in modern forests in the eastern Amazon. Together, our data provide a long-term example of past anthropogenic land use that can inform management and conservation efforts in modern Amazonian ecosystems.

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In the highlands of southern Brazil an anthropogenitcally driven expansion of forest occurred at the expense of grasslands between 1410 and 900 cal BP, coincident with a period of demographic and cultural change in the region. Previous studies have debated the relative contributions of increasing wetter and warmer climate conditions and human landscape modifications to forest expansion, but generally lacked high resoltiuon proxies to measure these effects, or have relied on single proxies to reconstruct both climate and vegetation. Here, we develop and test a model of natural ecosystem distribution against vegetation histories, paleoclimate proxies, and the archaeological record to distinguish human from temperature and precipitation impacts on the distribution and expansion of Araucaria forests during the late Holocene. Carbon isotopes from soil profiles confirm that in spite of climatic fluctuations, vegetation was stable and forests were spatially limited to south-facing slopes in the absence of human inputs. In contrast, forest management strategies for the past 1400 years expanded this economically important forest beyond its natural geographic boundaries in areas of dense pre-Columbian occupation, suggesting that landscape modifications were linked to demographic changes, the effects of which are still visible today.

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Archaeology provides few examples of large-scale fisheries at the frontier between catching and farming of fish. We analysed the spatial organization of earthen embankments to infer the functioning of a landscape-level pre-Columbian Amazonian fishery that was based on capture of out-migrating fish after reproduction in seasonal floodplains. Long earthen weirs cross floodplains. We showed that weirs bear successive V-shaped features (termed 'Vs' for the sake of brevity) pointing downstream for outflowing water and that ponds are associated with Vs, the V often forming the pond's downstream wall. How Vs channelled fish into ponds cannot be explained simply by hydraulics, because Vs surprisingly lack fishways, where, in other weirs, traps capture fish borne by current flowing through these gaps. We suggest that when water was still high enough to flow over the weir, out-migrating bottom-hugging fish followed current downstream into Vs. Finding deeper, slower-moving water, they remained. Receding water further concentrated fish in ponds. The pond served as the trap, and this function shaped pond design. Weir-fishing and pond-fishing are both practiced in African floodplains today. In combining the two, this pre-Columbian system appears unique in the world.

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A harmful algal bloom (HAB) of the raphidophyta alga Pseudochattonella cf. verruculosa during the 2016 austral summer (February-March) killed nearly 12% of the Chilean salmon production, causing the worst mass mortality of fish and shellfish ever recorded in the coastal waters of western Patagonia. The HAB coincided with a strong El Niño event and the positive phase of the Southern Annular Mode that altered the atmospheric circulation in southern South America and the adjacent Pacific Ocean. This led to very dry conditions and higher than normal solar radiation reaching the surface. Using time series of atmospheric, hydrologic and oceanographic data we show here that an increase in surface water temperature and reduced freshwater input resulted in a weakening of the vertical stratification in the fjords and sounds of this region. This allowed the advection of more saline and nutrient-rich waters, ultimately resulting in an active harmful algal bloom in coastal southern Chile.

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The development of agriculture is one of humankind's most pivotal achievements. Questions about plant domestication and the origins of agriculture have engaged scholars for well over a century, with implications for understanding its legacy on global subsistence strategies, plant distribution, population health and the global methane budget. Rice is one of the most important crops to be domesticated globally, with both Asia (Oryza sativa L.) and Africa (Oryza glaberrima Steud.) discussed as primary centres of domestication. However, until now the pre-Columbian domestication of rice in the Americas has not been documented. Here we document the domestication of Oryza sp. wild rice by the mid-Holocene residents of the Monte Castelo shell mound starting at approximately 4,000 cal. yr BP, evidenced by increasingly larger rice husk phytoliths. Our data provide evidence for the domestication of wild rice in a region of the Amazon that was also probably the cradle of domestication of other major crops such as cassava (Manihot esculenta), peanut (Arachis hypogaea) and chilli pepper (Capsicum sp.). These results underline the role of wetlands as prime habitats for plant domestication worldwide.

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Over 450 pre-Columbian (pre-AD 1492) geometric ditched enclosures ("geoglyphs") occupy ∼13,000 km2 of Acre state, Brazil, representing a key discovery of Amazonian archaeology. These huge earthworks were concealed for centuries under terra firme (upland interfluvial) rainforest, directly challenging the "pristine" status of this ecosystem and its perceived vulnerability to human impacts. We reconstruct the environmental context of geoglyph construction and the nature, extent, and legacy of associated human impacts. We show that bamboo forest dominated the region for ≥6,000 y and that only small, temporary clearings were made to build the geoglyphs; however, construction occurred within anthropogenic forest that had been actively managed for millennia. In the absence of widespread deforestation, exploitation of forest products shaped a largely forested landscape that survived intact until the late 20th century.

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A long held view about the occupation of southern proto-Jê pit house villages of the southern Brazilian highlands is that these sites represent cycles of long-term abandonment and reoccupation. However, this assumption is based on an insufficient number of radiocarbon dates for individual pit houses. To address this problem, we conducted a programme of comprehensive AMS radiocarbon dating and Bayesian modelling at the deeply stratified oversized pit House 1, Baggio I site (Cal. A.D. 1395-1650), Campo Belo do Sul, Santa Catarina state, Brazil. The stratigraphy of House 1 revealed an unparalleled sequence of twelve well preserved floors evidencing a major change in occupation dynamics including five completely burnt collapsed roofs. The results of the radiocarbon dating allowed us to understand for the first time the occupation dynamics of an oversized pit house in the southern Brazilian highlands. The Bayesian model demonstrates that House 1 was occupied for over two centuries with no evidence of major periods of abandonment, calling into question previous models of long-term abandonment. In addition, the House 1 sequence allowed us to tie transformations in ceramic style and lithic technology to an absolute chronology. Finally, we can provide new evidence that the emergence of oversized domestic structures is a relatively recent phenomenon among the southern proto-Jê. As monumental pit houses start to be built, small pit houses continue to be inhabited, evidencing emerging disparities in domestic architecture after AD 1000. Our research shows the importance of programmes of intensive dating of individual structures to understand occupation dynamics and site permanence, and challenges long held assumptions that the southern Brazilian highlands were home to marginal cultures in the context of lowland South America.

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The formation, functioning and emergent properties of patterned landscapes have recently drawn increased attention, notably in semi-arid ecosystems. We describe and analyze a set of similarly spectacular landforms in seasonal tropical wetlands. Surales landscapes, comprised of densely packed, regularly spaced mounds, cover large areas of the Orinoco Llanos. Although descriptions of surales date back to the 1940's, their ecology is virtually unknown. From data on soil physical and chemical properties, soil macrofauna, vegetation and aerial imagery, we provide evidence of the spatial extent of surales and how they form and develop. Mounds are largely comprised of earthworm casts. Recognizable, recently produced casts account for up to one-half of total soil mass. Locally, mounds are relatively constant in size, but vary greatly across sites in diameter (0.5-5 m) and height (from 0.3 m to over 2 m). This variation appears to reflect a chronosequence of surales formation and growth. Mound shape (round to labyrinth) varies across elevational gradients. Mounds are initiated when large earthworms feed in shallowly flooded soils, depositing casts that form 'towers' above water level. Using permanent galleries, each earthworm returns repeatedly to the same spot to deposit casts and to respire. Over time, the tower becomes a mound. Because each earthworm has a restricted foraging radius, there is net movement of soil to the mound from the surrounding area. As the mound grows, its basin thus becomes deeper, making initiation of a new mound nearby more difficult. When mounds already initiated are situated close together, the basin between them is filled and mounds coalesce to form larger composite mounds. Over time, this process produces mounds up to 5 m in diameter and 2 m tall. Our results suggest that one earthworm species drives self-organizing processes that produce keystone structures determining ecosystem functioning and development.

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