The nitrogen isotopic composition (δ 15 N) of amino acids is potentially useful as an alternative method for estimating the trophic levels of organisms in food webs. However, because this "amino acid method" has been constructed from the observations of only a few case studies of food-consumer combinations in previous studies, the universality of the approach remains unclear. In this study, we investigated the δ 15 N signatures of amino acids in 17 photoautotrophs and the trophic relationships during four controlled feeding experiments using green algae, zooplankton, and fish. The results are consistent with those reported in previous studies, implying that the amino acid method can be applied to a variety of organisms. From these and previously published data, we estimate the two factors (β, isotope differences among amino acids in primary producers; Δ, the 15 N-enrichment factor for each trophic level) required to calculate the trophic level. Based on the lowest error (1σ = 0.12) in the estimated trophic level, we conclude that a comparison of the δ 15 N values for glutamic acid and phenylalanine is most useful in calculating precise estimates of the trophic level, using the following equation: trophic level (TL Glu/Phe ) = (δ 15 N Glu -δ 15 N Phe -3.4)/7.6 + 1.
Setting out to isolate uncultivated deep marine sediment microorganisms, we engineered and operated a methane-fed continuous-flow bioreactor system for more than 2,000 days to enrich such organisms from anaerobic marine methane-seep sediments 15 (Supplementary Note 1). We successfully enriched many phylogenetically diverse yetto-be cultured microorganisms, including Asgard archaea members (Loki-, Heimdall-and Odinarchaeota) 15. For further enrichment and isolation, samples of the bioreactor community were inoculated in glass tubes with simple substrates and basal medium. After approximately one year, we found faint cell turbidity in a culture containing casamino acids supplemented with four bacteria-suppressing antibiotics (Supplementary Note 2) that was incubated at 20 °C. Clone librarybased small subunit (SSU) rRNA gene analysis revealed a simple community that contained Halodesulfovibrio and a small population of Lokiarchaeota (Extended Data Table 1). In pursuit of this archaeon, which we designated strain MK-D1, we repeated subcultures when MK-D1 reached maximum cell densities as measured by quantitative PCR (qPCR). This approach gradually enriched the archaeon, which has an extremely slow growth rate and low cell yield (Fig. 1a). The culture consistently had a 30-60-day lag phase and required more
A deep sleep in coal beds Deep below the ocean floor, microorganisms from forest soils continue to thrive. Inagaki et al. analyzed the microbial communities in several drill cores off the coast of Japan, some sampling more than 2 km below the seafloor (see the Perspective by Huber). Although cell counts decreased with depth, deep coal beds harbored active communities of methanogenic bacteria. These communities were more similar to those found in forest soils than in other deep marine sediments. Science , this issue p. 420 ; see also p. 376
Compound-specific isotopic analysis of amino acids (CSIA-AA) has emerged in the last decade as a powerful approach for tracing the origins and fate of nitrogen in ecological and biogeochemical studies. This approach is based on the empirical knowledge that source AAs (i.e., phenylalanine), fractionate 15 N very little (<0.5‰) during trophic transfer, whereas trophic AAs (i.e., glutamic acid), are greatly (~6-8‰) enriched in 15 N during each trophic step. The differential fractionation of these two AA groups can provide a valuable estimate of consumer trophic position that is internally indexed to the baseline δ 15 N value of the integrated food web. In this paper, we critically review the analytical methods for determining the nitrogen isotopic composition of AAs by gas chromatography/isotope-ratio mass spectrometry. We also discuss methodological considerations for accurate trophic position assessment of organisms using CSIA-AA. We then discuss the advantages and challenges of the CSIA-AA approach by examining published studies including trophic position assessment in various ecosystems, reconstruction of ancient human diets, reconstruction of animal migration and environmental variability, and assessment of marine organic matter dynamics. It is clear that the CSIA-AA approach can provide unique insight into the sources, cycling, and trophic modification of organic nitrogen as it flows through systems. However, some uncertainty still exists in how biochemical, physiological, and ecological mechanisms affect isotopic fractionation of trophic AAs. We end this review with a call for continued exploration of the mechanisms of AA isotopic fractionation, through various studies to promote the evolution of the rapidly growing field of CSIA-AA.
The abundance, diversity, activity, and composition of microbial communities in sulfide structures both of active and inactive vents were investigated by culture-independent methods. These sulfide structures were collected at four hydrothermal fields, both on-and off-axis of the back-arc spreading center of the Southern Mariana Trough. The microbial abundance and activity in the samples were determined by analyzing total organic content, enzymatic activity, and copy number of the 16S rRNA gene. To assess the diversity and composition of the microbial communities, 16S rRNA gene clone libraries including bacterial and archaeal phylotypes were constructed from the sulfide structures. Despite the differences in the geological settings among the sampling points, phylotypes related to the Epsilonproteobacteria and cultured hyperthermophilic archaea were abundant in the libraries from the samples of active vents. In contrast, the relative abundance of these phylotypes was extremely low in the libraries from the samples of inactive vents. These results suggest that the composition of microbial communities within sulfide structures dramatically changes depending on the degree of hydrothermal activity, which was supported by statistical analyses. Comparative analyses suggest that the abundance, activity and diversity of microbial communities within sulfide structures of inactive vents are likely to be comparable to or higher than those in active vent structures, even though the microbial community composition is different between these two types of vents. The microbial community compositions in the sulfide structures of inactive vents were similar to those in seafloor basaltic rocks rather than those in marine sediments or the sulfide structures of active vents, suggesting that the microbial community compositions on the seafloor may be constrained by the available energy sources. Our findings provide helpful information for understanding the biogeography, biodiversity and microbial ecosystems in marine environments.
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