## 1 Introduction  
Nitrogen is one of the basic elements that make up bacterial cell macromolecules, such as proteins, nucleic acids, and cell walls. Nitrogen-mediated regulation in bacteria is a complex regulatory network involving many signal transduction and effector proteins. In response to nitrogen starvation, some bacteria directly activate the transcription of genes associated with scavenging and transport systems for alternative nitrogen sources, catabolism of nitrogenous compounds, and the glutamine biosynthesis pathway [1, 2, 3]. Moreover, the stringent response mediated by RelA (encoding the alarmone ppGpp synthase) also plays a critical role in the bacterial adaptation to starvation and stress [4, 5, 6]. Under the condition of nitrogen-limitation stress, the nitrogen regulated (Ntr) response and the stringent reaction can be directly coupled [7, 8]. These studies have been intensively performed in enterobacteria, whereas little is known about how an environmental _Pantoea_ strain responds to nitrogen-limitation stress.  
Endophyte refers to the bacteria, actinomyces, or fungi which live in normal plant organs or tissues and do not cause obvious symptoms of external infection in the host plants [9]. The endophyte is a natural component of the plant microecosystem. The co-evolution of endophytes and host plants has shaped the unique genetic characteristics and metabolites of endophytes. In the process of co-evolution, endophytes not only meet the needs of their own survival but also enhance the adaptability of the host to the external environment [10; 11; 12], thus playing an important role in the growth and development of the host plants and their resistance to adverse environments [13; 14]. So far, endophytes such as _Bacillus_, _Pantoea_, _Pseudomonas_, and _Burkholderia_ have been isolated from a variety of plants for extensive studies and potential development [15; 16; 17; 18; 19].  
_Pantoea_ is a genus of Gram-negative bacterial endophytes that are widely found in plant tissues, intercellular spaces, cortical cells, xylem, and soil [20; 21; 22]. _Pantoea_ species can have beneficial effects on plants in a variety of ways [23; 24]. For instance, firstly, _Pantoea_ can secrete auxin (IAA), cytokinin (CTK), gibberellia (GA4), abscisic acid (ABA) [25] and induce plant system stress resistance [20; 26] to directly regulate the plant's growth. Secondly, _Pantoea_ can produce a variety of antimicrobial substances to inhibit the growth of many pathogenic microorganisms, which thus indirectly promotes plant production [27; 28; 29; 30; 31; 32]. Thirdly, _Pantoea_ can help plant tissue cells to obtain necessary nutrient elements; for example, _Pantoea_ spp. not only show the capability of dissolving insoluble phosphates [33; 34] but also have the ability for biological nitrogen fixation [35; 36; 37]. In addition, _Pantoea_ has been shown to induce systemic resistance and protection against phytopathogens in cultivated plants [38; 39; 40].  
So far, research on _Pantoea_ species has mainly focused on their effect on crops, with only a few reports on forestry applications [19]. In our previous studies, we isolated a pine growth-promoting bacterium, _P. eucalypt_ FBS135, from the branches of _Pine massonia_, which was identified as _Pantoee eucalypt_ by phylogenetic analysis. We found that FBS135 had an obvious growth-promoting effect on pine growth [41] and a remarkable tolerance to low levels of nitrogen, as it can grow in different media containing no nitrogen sources. We have demonstrated that FBS135 does not possess the ability of nitrogen fixation [42]. We hypothesize that FBS135 may have specific genes/mechanisms involved in its tolerance to low nitrogen nutrition, therefore, in this study, we examined the transcriptome of FBS135 upon nitrogen deprivation and exploited a transposon library for the functional genes and metabolic pathways involved in nitrogen starvation. This work provided insight into the molecular basis of how a _Pantoea_ endophyte adapts to nitrogen scarcity in the environment.