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Along with ceramics production, sedentism, and herding, agriculture is a major component of the Neolithic as it is defined in Europe. Therefore, the agricultural system of the first Neolithic societies and the dispersal of exogenous cultivated plants to Europe are the subject of many scientific studies. To work on these issues, archaeobotanists rely on residual plant remains—crop seeds, weeds, and wild plants—from archaeological structures like detritic pits, and, less often, storage contexts. To date, no plant with an economic value has been identified as domesticated in Western Europe except possibly opium poppy. The earliest seeds identified at archaeological sites dated to about 5500–5200 bc in the Mediterranean and Temperate Europe. The cultivated plants identified were cereals (wheat and barley), oleaginous plant (flax), and pulses (peas, lentils, and chickpeas). This crop package originated in the Fertile Crescent, where it was clearly established around 7500 bc (final Pre-Pottery Neolithic B), after a long, polycentric domestication process. From the middle of the 7th millennium bc, via the Balkan Peninsula, the pioneer Neolithic populations, with their specific economies, rapidly dispersed from east to west, following two main pathways. One was the maritime route over the northwestern basin of the Mediterranean (6200–5300 bc), and the other was the terrestrial and fluvial route in central and northwestern continental Europe (5500–4900 bc). On their trajectory, the agropastoral societies adapted the Neolithic founder crops from the Middle East to new environmental conditions encountered in Western Europe.

The Neolithic pioneers settled in an area that had experienced a long tradition of hunting and gathering. The Neolithization of Europe followed a colonization model. The Mesolithic groups, although exploiting plant resources such as hazelnut more or less intensively, did not significantly change the landscape. The impact of their settlements and their activities are hardly noticeable through palynology, for example. The control of the mode of reproduction of plants has certainly increased the prevalence of Homo sapiens, involving, among others, a demographic increase and the ability to settle down in areas that were not well adapted to year-round occupation up to that point. The characterization of past agricultural systems, such as crop plants, technical processes, and the impact of anthropogenic activities on the landscape, is essential for understanding the interrelation of human societies and the plant environment. This interrelation has undoubtedly changed deeply with the Neolithic Revolution.

Agriculture is a significant source of methane, contributing about 12% of the global anthropogenic methane emissions. Major sources of methane from agricultural activities are fermentation in the reticulo-rumen of ruminant animals (i.e., enteric methane), fermentation in animal manure, and rice cultivation. Enteric methane is the largest agricultural source of methane and is mainly controlled by feed dry matter intake and composition of the animal diet (i.e., fiber, starch, lipids). Processes that lead to generation of methane from animal manure are similar to those taking place in the reticulo-rumen. Methane emissions from manure, however, are greatly influenced by factors such as manure management system and ambient temperature. Systems that handle manure as a liquid generate much more methane than systems in which manure is handled as a solid. Low ambient temperatures drastically decrease methane emissions from manure. Once applied to soil, animal manure does not generate significant amounts of methane. Globally, methane emissions from rice cultivation represent about 10% of the total agricultural greenhouse gas emissions. In the rice plant, methane dissolves in the soil water surrounding the roots, diffuses into the cell-wall water of the root cells, and is eventually released through the micropores in the leaves. Various strategies have been explored to mitigate agricultural methane emissions. Animal nutrition, including balancing dietary nutrients and replacement of fiber with starch or lipids; alternative sinks for hydrogen; manipulation of ruminal fermentation; and direct inhibition of methanogenesis have been shown to effectively decrease enteric methane emissions. Manure management solutions include solid-liquid separation, manure covers, flaring of generated methane, acidification and cooling of manure, and decreasing manure storage time before soil application. There are also effective mitigation strategies for rice that can be categorized broadly into selection of rice cultivars, water regime, and fertilization. Alternate wetting and drying and mid-season drainage of rice paddies have been shown to be very effective practices for mitigating methane emissions from rice production.

The Basin of Mexico is a key world region for understanding agricultural intensification and the development of ancient and historic cities and states. Archaeologists working in the region have had a long-standing interest in understanding the dynamics of interactions between society and environment and their research has been at the forefront of advances in both method and theory. The Basin of Mexico was the geopolitical core of the Aztec empire, the largest state in the history of Mesoamerica. Its growth was sustained by a complex economy that has been the subject of much research.

Two themes underlie a broad interest in the pre-Hispanic agriculture of the Basin of Mexico. First, how with a Neolithic technology did the Aztecs and their predecessors sustain the growth of large cites, dense rural populations, and the largest state system in the history of pre-Hispanic Mesoamerica? Second, what is the relationship of agricultural intensification and urbanization and state formation? Mesoamerica is the only world region where primary civilizations developed that lacked domestic herbivores for either food or transportation. Their farming depended entirely on human labor and hand tools but sustained large cities, dense populations, and complex social institutions. Intensive agriculture began early and was promoted by risk, ecological diversity, and social differentiation, and included irrigation, terracing, and drained fields (chinampas). Most farming was managed by smallholder households and local communities, which encouraged corporate forms of governance and collective action. Environmental impacts included erosion and deposition, but were limited compared with the degradation that took place in the colonial period.

The ancient Near East was one of the earliest centers of agriculture in the world, giving rise to domesticated herd animals, cereals, and legumes that today have become primary agricultural staples worldwide. Although much attention has been paid to the origins of agriculture, identifying when, where, and how plants and animals were domesticated, equally important are the social and environmental consequences of agriculture. Shortly after the advent of domestication, agricultural economies quickly replaced hunting and gathering across Mesopotamia, the Levant, and Anatolia. The social and environmental context of this transition has profound implications for understanding the rise of social complexity and incipient urbanism in the Near East.

Economic transformation accompanied the expansion of agriculture throughout small-scale societies of the Near East. These farmsteads and villages, as well as mobile pastoral groups, formed the backbone of agricultural production, which enabled tradable surpluses necessary for more expansive, community-scale economic networks. The role of such economies in the development of social complexity remains debated, but they did play an essential role in the rise of urbanism. Cities depended on agricultural specialists, including farmers and herders, to feed urban populations and to enable craft and ritual specializations that became manifest in the first cities of southern Mesopotamia. The environmental implications of these agricultural systems in the Mesopotamian lowlands, especially soil salinization, were equally substantial. The environmental implications of Mesopotamian agriculture are distinct from those accompanying the spread of agriculture to the Levant and Anatolia, where deforestation, erosion, and loss of biodiversity can be identified as the hallmarks of agricultural expansion.

Agriculture is intimately connected with the rise of territorial empires across the Near East. Such empires often controlled agricultural production closely, for both economic and strategic ends, but the methods by which they encouraged the production of specific agricultural products and the adoption of particular agricultural strategies, especially irrigation, varied considerably between empires. By combining written records, archaeological data from surveys and excavation, and paleoenvironmental reconstruction, together with the study of plant and animal remains from archaeological sites occupied during multiple imperial periods, it is possible to reconstruct the environmental consequences of imperial agricultural systems across the Near East. Divergent environmental histories across space and time allow us to assess the sustainability of the agricultural policies of each empire and to consider how resulting environmental change contributed to the success or failure of those polities.

South Asia possesses a unique Neolithic transition to agricultural domestication. India has received far less attention in the quest for evidence of early agriculture than other regions of the world traditionally recognized as “centers of domestication” such as southwest Asia, western Asia, China, Mesoamerica, South America, New Guinea, and Africa. Hunter-gatherers with agricultural production appeared around the middle of the Holocene, 4000 to 1500 bce, with the cultivation of domesticates and a correspondingly more sedentary lifestyle emerging at this time. Two thousand years ago South Asia was inhabited by farmers, with densely populated river valleys, coastal plains, urban populations, states, and even empires. While some of the crops that supported these civilizations had been introduced from other regions of the world, a large proportion of these crops had local origins from wild plants native to the subcontinent.

As a case study for the origins of agriculture, South Asia has much to offer archaeologists and environmental scientists alike for understanding domestication processes and local transitions from foraging to farming as well as the ways in which early farmers adapted to and transformed the environment and regional vegetation. Information exchange from distant farmers from other agricultural centers into the subcontinent cannot be ruled out. However, it is clear that local agricultural origins occurred via a series of processes, including the dispersal of pastoral and agro-pastoral peoples across regions, the local domestication of animals and plants and the adoption by indigenous hunter-gatherers of food production techniques from neighboring cultures. Indeed, it is posited that local domestication events in India were occurring alongside agricultural dispersals from other parts of the world in an interconnected mosaic of cultivation, pastoralism, and sedentism. As humans in South Asia increasingly relied on a more restricted range of plant species, they became entangled in an increasingly fixed trajectory that allowed greater food production levels to sustain larger populations and support their developing social, cultural and food traditions.

Driving forces for natural soil salinity and alkalinity are climate, rock weathering, ion exchange, and mineral equilibria reactions that ultimately control the chemical composition of soil and water. The major weathering reactions that produce soluble ions are tabled. Where evapotranspiration is greater than precipitation, downward water movement is insufficient to leach solutes out of the soil profile and salts can precipitate. Microbes involved in organic matter mineralization and thus the carbon, nitrogen, and sulfur biogeochemical cycles are also implicated. Seasonal contrast and evaporative concentration during dry periods accelerate short-term oxidation-reduction reactions and local and regional accumulation of carbonate and sulfur minerals. The presence of salts and alkaline conditions, together with the occurrence of drought and seasonal waterlogging, creates some of the most extreme soil environments where only specially adapted organisms are able to survive. Sodic soils are alkaline, rich in sodium carbonates, with an exchange complex dominated by sodium ions. Such sodic soils, when low in other salts, exhibit dispersive behavior, and they are difficult to manage for cropping. Maintaining the productivity of sodic soils requires control of the flocculation-dispersion behavior of the soil. Poor land management can also lead to anthropogenically induced secondary salinity. New developments in physical chemistry are providing insights into ion exchange and how it controls flocculation-dispersion in soil. New water and solute transport models are enabling better options of remediation of saline and/or sodic soils.

Soil salinity has been causing problems for agriculturists for millennia, primarily in irrigated lands. The importance of salinity issues is increasing, since large areas are affected by irrigation-induced salt accumulation. A wide knowledge base has been collected to better understand the major processes of salt accumulation and choose the right method of mitigation. There are two major types of soil salinity that are distinguished because of different properties and mitigation requirements. The first is caused mostly by the large salt concentration and is called saline soil, typically corresponding to Solonchak soils. The second is caused mainly by the dominance of sodium in the soil solution or on the soil exchange complex. This latter type is called “sodic” soil, corresponding to Solonetz soils. Saline soils have homogeneous soil profiles with relatively good soil structure, and their appropriate mitigation measure is leaching. Naturally sodic soils have markedly different horizons and unfavorable physical properties, such as low permeability, swelling, plasticity when wet, and hardness when dry, and their limitation for agriculture is mitigated typically by applying gypsum. Salinity and sodicity need to be chemically quantified before deciding on the proper management strategy. The most complex management and mitigation of salinized irrigated lands involves modern engineering including calculations of irrigation water rates and reclamation materials, provisions for drainage, and drainage disposal. Mapping-oriented soil classification was developed for naturally saline and sodic soils and inherited the first soil categories introduced more than a century ago, such as Solonchak and Solonetz in most of the total of 24 soil classification systems used currently. USDA Soil Taxonomy is one exception, which uses names composed of formative elements.