A primary aim of microbial ecology is to determine patterns and drivers of community distribution, interaction, and assembly amidst complexity and uncertainty. Microbial community composition has been shown to change across gradients of environment, geographic distance, salinity, temperature, oxygen, nutrients, pH, day length, and biotic factors 1-6 . These patterns have been identified mostly by focusing on one sample type and region at a time, with insights extra polated across environments and geography to produce generalized principles. To assess how microbes are distributed across environments globally-or whether microbial community dynamics follow funda mental ecological 'laws' at a planetary scale-requires either a massive monolithic cross environment survey or a practical methodology for coordinating many independent surveys. New studies of microbial environments are rapidly accumulating; however, our ability to extract meaningful information from across datasets is outstripped by the rate of data generation. Previous meta analyses have suggested robust gen eral trends in community composition, including the importance of salinity 1 and animal association 2 . These findings, although derived from relatively small and uncontrolled sample sets, support the util ity of meta analysis to reveal basic patterns of microbial diversity and suggest that a scalable and accessible analytical framework is needed.The Earth Microbiome Project (EMP, http://www.earthmicrobiome. org) was founded in 2010 to sample the Earth's microbial communities at an unprecedented scale in order to advance our understanding of the organizing biogeographic principles that govern microbial commu nity structure 7,8 . We recognized that open and collaborative science, including scientific crowdsourcing and standardized methods 8 , would help to reduce technical variation among individual studies, which can overwhelm biological variation and make general trends difficult to detect 9 . Comprising around 100 studies, over half of which have yielded peer reviewed publications (Supplementary Table 1), the EMP has now dwarfed by 100 fold the sampling and sequencing depth of earlier meta analysis efforts 1,2 ; concurrently, powerful analysis tools have been developed, opening a new and larger window into the distri bution of microbial diversity on Earth. In establishing a scalable frame work to catalogue microbiota globally, we provide both a resource for the exploration of myriad questions and a starting point for the guided acquisition of new data to answer them. As an example of using this Our growing awareness of the microbial world's importance and diversity contrasts starkly with our limited understanding of its fundamental structure. Despite recent advances in DNA sequencing, a lack of standardized protocols and common analytical frameworks impedes comparisons among studies, hindering the development of global inferences about microbial life on Earth. Here we present a meta-analysis of microbial community samples collected by hundreds of r...

The fine‐scale temporal dynamics of the chicken gut microbiome are unexplored, but thought to be critical for chicken health and productivity. Here, we monitored the fecal microbiome of healthy chickens on days 1–7, 10, 14, 21, 28, and 35 after hatching, and performed 16S rRNA amplicon sequencing in order to obtain a high‐resolution census of the fecal microbiome over time. In the period studied, the fecal microbiomes of the developing chickens showed a linear‐log increase in community richness and consistent shifts in community composition. Three successional stages were detected: the first stage was dominated by vertically transmitted or rapidly colonizing taxa including Streptococcus and Escherichia/Shigella; in the second stage beginning on day 4, these taxa were displaced by rapid‐growing taxa including Lachnospiraceae and Ruminococcus‐like species variants; and in the third stage, starting on day 10, slow‐growing, specialist taxa including Candidatus Arthrobacter and Romboutsia were detected. The patterns of displacement and the previously reported ecological characteristics of many of the dominant taxa observed suggest that resource competition plays an important role in regulating successional dynamics in the developing chicken gut. We propose that the boundaries between successional stages (3–4 and 14–21 days after hatching) may be optimal times for microbiome interventions.

Observations, atmosphere models forced by historical SSTs, and idealized simulations are used to determine the causes and mechanisms of interannual to multidecadal precipitation anomalies over southeast South America (SESA) since 1901. About 40% of SESA precipitation variability over this period can be accounted for by global SST forcing. Both the tropical Pacific and Atlantic Oceans share the driving of SESA precipitation, with the latter contributing the most on multidecadal time scales and explaining a wetting trend from the early midcentury until the end of the last century. Cold tropical Atlantic SST anomalies are shown to drive wet conditions in SESA. The dynamics that link SESA precipitation to tropical Atlantic SST anomalies are explored. Cold tropical Atlantic SST anomalies force equatorward-flowing upper-tropospheric flow to the southeast of the tropical heating anomaly, and the vorticity advection by this flow is balanced by vortex stretching and ascent, which drives the increased precipitation. The 1930s Pampas Dust Bowl drought occurred, via this mechanism, in response to warm tropical Atlantic SST anomalies. The atmospheric response to cold tropical Pacific SSTs also contributed. The tropical Atlantic SST anomalies linked to SESA precipitation are the tropical components of the Atlantic multidecadal oscillation. There is little evidence that the large trends over past decades are related to anthropogenic radiative forcing, although models project that this will cause a modest wetting of the climate of SESA. As such, and if the Atlantic multidecadal oscillation has shifted toward a warm phase, it should not be assumed that the long-term wetting trend in SESA will continue. Any reversal to a drier climate more typical of earlier decades would have clear consequences for regional agriculture and water resources. * Lamont-Doherty Earth Observatory Contribution Number 7383.

The precipitation history over the last century in the Catskill Mountains region that supplies water to New York City is studied. A severe drought occurred in the early to mid-1960s followed by a wet period that continues. Interannual variability of precipitation in the region is related to patterns of atmospheric circulation variability in the midlatitude east Pacific-North America-west Atlantic sector with no link to the tropics. Associated SST variations in the Atlantic are consistent with being forced by the anomalous atmospheric flow rather than being causal. In winter and spring the 1960s drought was associated with a low pressure anomaly over the midlatitude North Atlantic Ocean and northerly subsiding flow over the greater Catskills region that would likely suppress precipitation. The cold SSTs offshore during the drought are consistent with atmospheric forcing of the ocean. The subsequent wet period was associated with high pressure anomalies over the Atlantic Ocean and ascending southerly flow over eastern North America favoring increased precipitation and a strengthening of the Northern Hemisphere storm track. Neither the drought nor the subsequent pluvial are simulated in sea surface temperature-forced atmosphere GCMs. The long-term wetting is also not simulated as a response to changes in radiative forcing by coupled models. It is concluded that past precipitation variability in the region, including the drought and pluvial, were most likely caused by internal atmospheric variability. Such events are unpredictable and a drought like the 1960s one could return while the long-term wetting trend need not continue-conclusions that have implications for management of New York City's water resources.

The type and frequency of disturbances experienced by soil microbiomes is expected to increase given predicted global climate change scenarios and intensified anthropogenic pressures on ecosystems. While the direct effect of multiple disturbances to soil microbes has been explored in terms of function, their effect on the recovery of microbial community composition remains unclear. Here, we used soil microcosm experiments and multiple model disturbances to explore their short-term effect on the recovery of soil microbiota after identical or novel stresses. Soil microcosms were exposed to a heat shock to create an initial effect. Upon initial community recovery (25 days after stress), they were subjected to a second stress, either a heat or a cold shock, and they were monitored for additional 25 days. To carefully verify the bacterial response to the disturbances, we monitored changes in community composition throughout the experiment using 16S rRNA gene transcript amplicon sequencing. The application of a heat shock to soils with or without the initial heat shock resulted in similar successional dynamics, but these dynamics were faster in soils with a prior heat shock. The application of a cold shock had negligible effects on previously undisturbed soils but, in combination with an initial heat shock, caused the largest shift in the community composition. Our findings show that compounded perturbation affects bacterial community recovery by altering community structure and thus, the community’s response during succession. By altering dominance patterns, disturbance legacy affects the microbiome’s ability to recover from further perturbation within the 25 days studied. Our results highlight the need to consider the soil’s disturbance history in the development of soil management practices in order to maintain the system’s resilience.