Mediterranean Bathypelagic Habitat

In general, a remarkable number of similarities were found with the deep meso-pelagic Pacific and a convergence at the level of taxa found and types of metabolism with the soil microbiota is starting to be perceived. The authors use the term \"invisible soil\" paraphrasing the \"invisible forest\" coined by Paul Falkowski to refer to the hidden but gigantic primary productivity found in the photic zone. The diversity of metabolic enzymes involved in resilient organic compounds degradation was very high. However, many microbes could complement their heterotrophic metabolism with chemolithotrophic energy supplies and, specifically in the Mediterranean, the oxidation of carbon monoxide, probably released by tectonic activity, could be important. There is also evidence that the microbes rarely live isolated. The free living planktonic lifestyle is probably not very popular in this extremely depleted environment. Quorum sensing genes indicate that instead, microbes tend to aggregate in particles and they could become luminescent maybe to attract and be eaten by animals. This strategy could provide the cells with a sporadic visit to the nutritious oasis of an animal gut. Overall, this paper shows that the deep ocean possesses a rich and mostly unknown microbiota that deserves much more studies.

A recent analysis of a metagenomic library from the deep Mediterranean shows a surprising high number of quorum sensing or lux genes that are only expressed when bacteria live in colonies. The deep ocean might be too depleted in resources for microbes to live independently. Instead the association to detritus particles might give them a rich microenvironment. Now, some of the genes detected have been positively identified as luxA, directly involved in bioluminescence.

Why would deep sea bacteria be luminescent? One possible explanation is that they become attractive to animals that at these depths are very photosensitive. Being swallowed by one of these creatures would give the bacteria a temporary oasis of nutrient-rich conditions before another long dip in the abyssal black.

总体而言，研究发现其与太平洋深层中远洋区域存在显著相似性，且在分类群水平及代谢类型上与土壤微生物群（soil microbiota）的趋同性正逐渐被认知。作者借用Paul Falkowski提出的‘隐形森林’（invisible forest）概念，创造了‘隐形土壤’（invisible soil）这一术语，用以指代透光层中隐藏但巨大的初级生产力。参与难降解有机化合物分解的代谢酶多样性极高。然而，许多微生物可通过化能无机营养型能量供给补充其异养代谢（heterotrophic metabolism）；尤其在地中海区域，由构造活动释放的一氧化碳氧化过程可能具有重要意义。此外有证据表明，这些微生物极少单独生存。在这种极度贫瘠的环境中，自由生活的浮游生活方式可能并不普遍。群体感应基因（quorum sensing genes）表明，微生物反而倾向于聚集在颗粒中，且可能通过发光吸引动物并被其摄食。这种策略可使细胞偶尔进入动物肠道这一营养绿洲。总体而言，本研究表明深海拥有丰富且大多未知的微生物群，值得开展更多研究。
近期对地中海深层宏基因组文库（metagenomic library）的分析显示，群体感应基因或lux基因的数量高得惊人，这些基因仅在细菌形成菌落时表达。
深海细菌为何会发光？一种可能的解释是，它们对该深度高度光敏的动物具有吸引力。被这类生物吞食后，细菌可在再次陷入深渊黑暗之前，暂时进入营养丰富的环境绿洲。