Rainfall seasonality shapes microbial assembly and niche characteristics in Yunnan Plateau lakes, China.

Microorganisms are crucial components of freshwater ecosystems. Understanding the microbial community assembly processes and niche characteristics in freshwater ecosystems, which are poorly understood, is crucial for evaluating microbial ecological roles. The Yunnan Plateau lakes in China represent a freshwater ecosystem that is experiencing eutrophication due to anthropogenic activities. Here, variation in the assembly and niche characteristics of both prokaryotic and microeukaryotic communities was explored in Yunnan Plateau lakes across two seasons (dry season and rainy season) to determine the impacts of rainfall and environmental conditions on the microbial community and niche. The results showed that the environmental heterogeneity of the lakes decreased in the rainy season compared to the dry season. The microbial (bacterial and microeukaryotic) α-diversity significantly decreased during the rainy season. Deterministic processes were found to dominate microbial community assembly in both seasons. ß-Diversity decomposition analysis revealed that microbial community compositional dissimilarities were dominated by species replacement processes. The co-occurrence networks indicated reduced species complexity for microbes and a destabilized network for prokaryotes prior to rainfall, while the opposite was found for microeukaryotes following rainfall. Microbial niche breadth decreased significantly in the rainy season. In addition, lower prokaryotic niche overlap, but greater microeukaryotic niche overlap, was observed after rainfall. Rainfall and environmental conditions significantly affected the microbial community assembly and niche characteristics. It can be concluded that rainfall and external pollutant input during the seasonal transition alter the lake environment, thereby regulating the microbial community and niche in these lakes. Our findings offer new insight into microbiota assembly and niche patterns in plateau lakes, further deepening the understanding of freshwater ecosystem functioning.

Heterogeneous bacterial communities affected by phytoplankton community turnover and microcystins in plateau lakes of Southwestern China.

Both phytoplankton and bacteria are fundamental organisms with key ecological functions in lake ecosystems. However, the mechanistic interactions through which phytoplankton community change and bacterial communities interact remain poorly understood. Here, the responses of bacterial communities to the community structure, resource-use efficiency (RUE), and community turnover of phytoplankton and microcystins (MCs) were investigated in Lake Dianchi, Lake Xingyun, and Lake Erhai of Southwestern China across two seasons (May and October 2020). Among phytoplankton, Cyanobacteria was the dominant species in all three lakes and attained greater dominance in October than in May due to variation in the RUE of nitrogen and phosphorus and environmental changes. The production of MCs, including MC_LR, MC_RR and MC_YR, was the result of the massive Cyanobacteria. Decreases in diversity and increases in heterogeneity were observed in the bacterial community structure. Nutrient levels, environmental factors and MCs (especially MC_YR) jointly affected the bacterial community in lakes, namely its diversity and community assembly. The cascading effects in lakes mediated by environmental conditions, phytoplankton community composition, RUE, community turnover, and MCs on bacterial communities were revealed in this study. These findings underscore the importance of relating phytoplankton community change and MCs to the bacterial community, which is fundamental for better understanding the lake ecosystem functioning and potential risks of MCs.

Earliest systematic coal exploitation for fuel extended to ~3600 B.P.

Coal has long fueled human civilizations. The history of systematic coal fuel exploitation has been traced back to the late third millennium before present (post-2500 B.P.). Although sporadic combustion of coal for fuel was reported in some prehistoric archaeological sites, evidence for the systematic exploitation of coal for fuel before 2500 B.P. remains lacking. Here, we report comprehensive understanding for the earliest systematic exploitation of coal for fuel at the Jirentaigoukou site in Xinjiang, northwestern China, at ~3600 B.P. The main body of the site witnessed systematic exploitation of bituminous coals, illustrating a complete chaîne opératoire with selective mining, planned storage, and extensive combustion. Our results transform the knowledge of energy history by extending the upper limit of the systematic exploitation of coal for fuel by approximately a millennium, and provide a precedent of energy transition under intense conflict between social demand and environmental deterioration.

Using multiple normalization procedures and contamination indices in the assessment of trace metal(loid) contents of the surface sediments of Lake Xingyun, southwestern China.

Trace metal(loid) (TM) contamination, especially of aquatic ecosystems, is a global ongoing environmental problem. Fully and accurately determining their anthropogenic sources is a key requirement for formulating remediation and management strategies. Herein, we developed a multiple normalization procedure, combined with principal component analysis (PCA) to assess the influence of data-treatment and environmental factors on the traceability of TMs in surface sediments of Lake Xingyun, China. Multiple contamination indices, i.e., Enrichment factor (EF), Pollution Load Index (PLI), Pollution Contribution Rate (PCR) and Exceeded multiple discharge standard limits (BSTEL) suggest that contamination is dominated by Pb with the average EF exceed 3, especially within the estuary aeras with the PCR >40 %. The analysis demonstrates that the mathematical normalization of data, which adjusts it for various geochemical influences, has a significant effect on analysis outputs and interpretation. Routine (Log) and extreme (outlier removing) transformations may mask and skew important information contained within the original (raw) data, which create biased or meaningless principal components. Granulometric and geochemical normalization procedures can obviously identify the influence of grain size and other environmental impact on TM contents in principal components, but incorrectly explains the potential sources and contamination on different sites. Reducing the influence of organic matter by normalization allowed the mineralogy, bio-degradation, salinity, and anthropogenic sources associated with local sewage and anthropogenic smelting to be identified and interpreted more clearly. Moreover, the co-occurrence network analysis also confirms that the influence of grain size, salinity, and organic matter content are the primary factors controlling the spatial variability in the type and concentrations of TMs.

Recent water-level fluctuations, future trends and their eco-environmental impacts on Lake Qinghai.

The water level of Lake Qinghai, the largest lake on the Qinghai-Tibetan Plateau, has increased continuously, at an average speed of 0.21 m per year since 2005, causing a rapid expansion of the lake area. We investigated the hydrological processes of Lake Qinghai and the surrounding watershed that have influenced water level and lake area from 1956 to 2019. Relationships among water level, climate change and human activities were also assessed. Water level and lake area were positively correlated with precipitation and runoff into the lake, and negatively correlated with evaporation. Climate change factors including precipitation and runoff were the primary causes of lake level change, whereas human activities, including variation in a human footprint index, land use, and grassland irrigation, were secondary factors. A time series model forecasted that from 2020 to 2050 water levels will increase further by 2.45 m. Although this increase in water level may have some benefits, such as reduced local desertification, the expansion of lake area will continue to flood low beaches, pasture lands, near shore infrastructure and roads, and impact tourism locations. However, continued water level rise may also have negative ecological effects, such as reduce habitat of seasonal birds and reduced water quality due to erosion and sediment resuspension in shallow nearshore lake areas. Local stakeholders, government authorities, and scientists should give greater attention to anticipated changes in water level, and further ecological studies and infrastructure adaptation measures should be implemented.

Sedimentary DNA for tracking the long-term changes in biodiversity.

Understanding long-term dynamics is vitally important for explaining current biodiversity patterns and setting conservation goals in a changing world. However, the changes in biodiversity in time and space, particularly the dynamics at the centuries or even longer time scales, are poorly documented because of a lack of continuous monitoring data. The sedimentary DNA (sedDNA) has a great potential for paleo-community reconstruction, and it has recently been used as a powerful tool to characterize past dynamics in terms of biodiversity over geological timescales. In particular, it is useful for prokaryotes and eukaryotes that do not fossilize; hence, it is revolutionizing the scope of paleoecological research. Here, a "Research Weaving" method was performed with systematic maps and bibliometric webs based on the Web of Science for Science Citation Index Expanded, presenting a comprehensive landscape of the sedDNA that traces biological dynamics. We identified that most sedDNA-based studies have focused on microbial dynamics and on using samples from multitypes of sediments. This review summarized the advantages and common applications of sedDNA, focused on the biodiversity in microbial communities, and provided an outlook for the future of sedDNA research.

How Human Subsistence Strategy Affected Fruit-Tree Utilization During the Late Neolithic and Bronze Age: Investigations in the Northeastern Tibetan Plateau.

The history of fruit-tree utilization by prehistoric people has become an important issue that has attracted increasing attention in recent years. However, the question of how people used fruit trees has not yet been answered; in particular, the impacts of different subsistence strategies on human behavior regarding fruit-tree utilization (wild gathering or conscious cultivation) have not yet been considered. Here, we present the results of charcoal identification of fruit trees from 16 dated archeological sites in the northeastern Tibetan Plateau (NETP) spanning the period c. 5,200-2,600 BP. We combine this with reported multidisciplinary evidence to explore the history of fruit-tree utilization as well as its relation to the subsistence strategy in the NETP during the late Neolithic and Bronze Age. Our results demonstrate that Rosaceae [Prunus L., Prunus Padus L., Maloideae L., and Malus baccata (L.) Borkh], Elaeagnaceae (Hippophae L. and Elaeagnus angustifolia L.), and Rhamnaceae (only Ziziphus Mill.) were used by people in the NETP, and there was a downward trend in the use of fruit trees during the late Neolithic and Bronze Age. This is in notable contrast to the situation in the Chinese Loess Plateau in the parallel period. The cold-dry climate during the Bronze Age seemed to be one of the reasons. The fruit trees used by people in the NETP were likely gathered from the wild rather than consciously cultivated, and the subsistence strategy of agropastoralism may have played a significant role during the processes.

eDNA revealed in situ microbial community changes in response to Trapa japonica in Lake Qionghai and Lake Erhai, southwestern China.

Trapa japonica was observed to have inhibiting effects and could be used as a potential environment-friendly control strategy for cyanobacterial blooms in freshwater. However, the changes and effecting mechanisms in eukaryotic and prokaryotic communities by T. japonica are not yet clear. In this study, the effects of T. japonica on microbial communities were assessed in Lake Qionghai and Lake Erhai by 18S rRNA and 16S rRNA amplicon sequencing, respectively. The results showed that T. japonica can improve biodiversity and change the microbial community structures to varying degrees in both lakes. The alpha diversity indexes of microbial communities (e.g., Shannon, Sobs, Ace and Chao 1) were higher in the water inhabited by T. japonica (TJ group) than the water uninhabited by T. japonica (control) (P < 0.05). The PCoA results suggested that the microbial community compositions differed between the two groups (PERMANOVA P = 0.001). In Lake Qionghai, the relative abundances of dominant taxa and nutrients level showed little differences between the two groups. These may result from the homogenous water condition in Lake Qionghai. While the genera Cyanobium_PCC-6307, the majority of Cyanobacteria, decreased significantly in TJ group than control according to 16S rRNA gene sequencing. In Lake Erhai, environmental variables were distinctly affected by T. japonica, which was found to drive Cryptophyceae to become the main taxa through taxonomic analysis of 18S rRNA. Based on 16S rRNA gene sequencing, T. japonica reduced the relative abundance of Cyanobacteria, such as Planktothrix_NIVA-CYA_15 and Cyanobium_PCC-6307, by enriching cyanobactericidal bacteria and growth-inhibiting bacteria (e.g., Limnohabitans and Flavobacterium) and changing environmental parameters. Our results revealed that T. japonica acts in shaping microbial communities in lakes on the community level, shedding new lights on eutrophication mitigation, one of the most serious global ecological problems we are facing.

In-situ responses of phytoplankton to graphene photocatalysis in the eutrophic lake Xingyun, southwestern China.

Graphene photocatalysis is receiving increased attention for its potential to be used as a novel green technology for mitigating harmful algae in highly eutrophic waters. However, graphene is seldom applied to in situ aquatic ecosystems for environmental applications. Here, the impacts of graphene photocatalysis on phytoplankton and environmental conditions were evaluated through an in situ macrocosm experiment in the eutrophic Lake Xingyun, southwestern China. The graphene photocatalysis treated area had significantly reduced conductivity, total nitrogen (TN), total phosphorus (TP) and dissolved phosphorus concentrations, as well as increased dissolved oxygen (DO) concentrations. The abundances of all species of the genus Microcystis were significantly reduced in the graphene photocatalysis-treated area; in contrast, the abundances of all species of the diazotrophic genera, including Anabaena and Aphanizomenon, greatly increased after treatment with graphene photocatalysis. Eukaryotic algae, especially Chlorophyta, Euglenophyta and Pyrrophyta, as well as Cryptophyta, had significantly higher abundances in the graphene photocatalysis-treated area, whereas most of the eutrophic diatom species had lower abundances in the treated area. These observed differences in eukaryotic algae between the two groups might be related to their sensitivity to graphene photocatalysis and their tolerance of nutrients. Generally, graphene photocatalysis can make a great contribution to the improvement of eutrophic water, as evidenced by the reduction in cyanobacteria abundance and phosphorus concentration, as well as the increase in species richness and the dissolved oxygen concentration in the treated area. However, the mechanisms underlying these differences in phytoplankton community structure and environmental conditions require further study.

A Review and Perspective of eDNA Application to Eutrophication and HAB Control in Freshwater and Marine Ecosystems.

Changing ecological communities in response to anthropogenic activities and climate change has become a worldwide problem. The eutrophication of waterbodies in freshwater and seawater caused by the effects of human activities and nutrient inputs could result in harmful algae blooms (HABs), decreases water quality, reductions in biodiversity and threats to human health. Rapid and accurate monitoring and assessment of aquatic ecosystems are imperative. Environmental DNA (eDNA) analysis using high-throughput sequencing has been demonstrated to be an effective and sensitive assay for detecting and monitoring single or multiple species in different samples. In this study, we review the potential applications of eDNA approaches in controlling and mitigating eutrophication and HABs in freshwater and marine ecosystems. We use recent studies to highlight how eDNA methods have been shown to be a useful tool for providing comprehensive data in studies of eutrophic freshwater and marine environments. We also provide perspectives on using eDNA techniques to reveal molecular mechanisms in biological processes and mitigate eutrophication and HABs in aquatic ecosystems. Finally, we discuss the feasible applications of eDNA for monitoring biodiversity, surveying species communities and providing instructions for the conservation and management of the environment by integration with traditional methods and other advanced techniques.

Neolithic millet farmers contributed to the permanent settlement of the Tibetan Plateau by adopting barley agriculture.

The permanent human settlement of the Tibetan Plateau (TP) has been suggested to have been facilitated by the introduction of barley agriculture ∼3.6 kilo-years ago (ka). However, how barley agriculture spread onto the TP remains unknown. Given that the lower altitudes in the northeastern TP were occupied by millet cultivators from 5.2 ka, who also adopted barley farming ∼4 ka, it is highly possible that it was millet farmers who brought barley agriculture onto the TP ∼3.6 ka. To test this hypothesis, we analyzed mitochondrial DNA (mtDNA) from 8277 Tibetans and 58 514 individuals from surrounding populations, including 682 newly sequenced whole mitogenomes. Multiple lines of evidence, together with radiocarbon dating of cereal remains at different elevations, supports the scenario that two haplogroups (M9a1a1c1b1a and A11a1a), which are common in contemporary Tibetans (20.9%) and were probably even more common (40-50%) in early Tibetans prior to historical immigrations to the TP, represent the genetic legacy of the Neolithic millet farmers. Both haplogroups originated in northern China between 10.0-6.0 ka and differentiated in the ancestors of modern Tibetans ∼5.2-4.0 ka, matching the dispersal history of millet farming. By showing that substantial genetic components in contemporary Tibetans can trace their ancestry back to the Neolithic millet farmers, our study reveals that millet farmers adopted and brought barley agriculture to the TP ∼3.6-3.3 ka, and made an important contribution to the Tibetan gene pool.

Asian archaeology. Response to Comment on "Agriculture facilitated permanent human occupation of the Tibetan Plateau after 3600 B.P.".

Guedes et al. have drawn attention to a mismatch between the predictions of their "thermal niche model" and the records we have published of early barley finds in the northeastern Tibetan Plateau. Here, we consider how that mismatch usefully draws our attention to the additional variables that may account for it-namely, variations in genetic expression and agricultural practice.